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16 pages, 3082 KB  
Article
Wnt and Treg-Associated Signaling Coordinate Mucosal Regeneration and MALT Formation in a Mouse Model of Chronic Colitis
by Nanami Watanabe, Mio Kobayashi, Tatsu Kuriki, Yuri Ebizuka, Mai Hirata, Rintaro Mizuguchi, Mio Takimoto, Bai Yidan, Mengyuan Luo, Mai Todoroki, Ma Suzanneth G. Lola, Xinyu Zou, Sha Jiang, Tetsuhito Kigata, Makoto Shibutani, Toshinori Yoshida and Tsutomu Omatsu
Int. J. Mol. Sci. 2026, 27(2), 779; https://doi.org/10.3390/ijms27020779 - 13 Jan 2026
Viewed by 84
Abstract
Chronic ulcerative colitis disrupts mucosal-acquired immunity; however, the relationship between mucosal regeneration and mucosa-associated lymph tissue (MALT) development remains unclear. We explored crypt responses, MALT phenotypes, and regulatory T cells (Tregs) in a mouse model of chronic colitis following two cycles of dextran [...] Read more.
Chronic ulcerative colitis disrupts mucosal-acquired immunity; however, the relationship between mucosal regeneration and mucosa-associated lymph tissue (MALT) development remains unclear. We explored crypt responses, MALT phenotypes, and regulatory T cells (Tregs) in a mouse model of chronic colitis following two cycles of dextran sodium sulfate (DSS) exposure. The mucosal regeneration score correlated with crypt expression of Ki-67 and LGR5, submucosal FOXP3-positive Treg expression, and MALT scores. MALT can be categorized into solitary-isolated lymphoid structures, tertiary lymphoid structures, and colonic patches. Regenerative crypts adjacent to tertiary lymphoid structures exhibit reduced expression of Ki-67, LGR5, and SOX9, which might favor mucosal differentiation. These findings were further supported by correlations between crypt stem cell- and Treg-related colonic gene expression of Lgr5, Sox9, Wnt6, Ccl20, and IL10, and between Tgfb1 and Cxcl13. These results suggested that chronic colitis is repaired by stem cell-mediated mucosal regeneration and differentiation, potentially driven by the development of MALT-containing Tregs. Full article
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16 pages, 2466 KB  
Article
Regenerative and Dermal Wound Healing Activities of Bioactive Octapeptide
by Shan Lakmal Edirisinghe, Chamilani Nikapitiya and Mahanama De Zoysa
Cosmetics 2026, 13(1), 16; https://doi.org/10.3390/cosmetics13010016 - 13 Jan 2026
Viewed by 185
Abstract
Cosmeceutical peptides (CPs), which modulate various biological activities, including skin regeneration and wound healing, have emerged as promising agents in skincare. In this study, we investigated the regenerative and wound healing potential of a short peptide, CP-02 (sequence CDARSDAR), using human dermal fibroblast [...] Read more.
Cosmeceutical peptides (CPs), which modulate various biological activities, including skin regeneration and wound healing, have emerged as promising agents in skincare. In this study, we investigated the regenerative and wound healing potential of a short peptide, CP-02 (sequence CDARSDAR), using human dermal fibroblast cells (HDFs) in vitro and a zebrafish model in vivo. In HDFs, CP-02 treatment at concentrations of 50, 100, and 200 µg/mL significantly accelerated wound closure in a dose-dependent manner (p < 0.05) and upregulated the mRNA expression of CCND1, MYC, FGF2, EFG, and IL-8 at 12 h post-treatment. In amputated zebrafish larvae, exposure to CP-02 (5 µg/mL) for 72 h significantly increased fin regeneration, with a fin area of 3.5 mm2 and fin-fold length of 0.2 mm, compared with those in controls (2 mm2 and 0.07 mm, respectively). Intramuscular administration of CP-02 significantly improved the healing rates in wounded adult zebrafish to 58% and 76% on 12 and 16 days post wounding (dpw), respectively, compared with the vehicle (35% and 44%, respectively). Histological analysis (H&E staining) revealed reduced inflammatory cell infiltration, complete granulation, and re-epithelialization in the CP-02-treated tissues at 12 dpw. Furthermore, mRNA expression levels of tnf-α, il-1β, tgfb1, mmp9, mmp13, and timp2b were elevated in the CP-02 group at 4 dpw, whereas those of pro-fibrotic mediators, including acta2, ctgfb, cdh1, and col9a3 reduced in muscle tissue on 12 dpw. Collectively these findings demonstrate that CP-02 promotes effective, scar-reducing regeneration and wound healing, highlighting its strong potential as a therapeutic peptide for future skincare and cosmeceutical applications. Full article
(This article belongs to the Section Cosmetic Dermatology)
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20 pages, 4492 KB  
Article
Integrated Analysis of Testicular Histology, Sperm Quality, and Gene Expression (TGFB2, DMRT1) in Rooster Semen (Gallus gallus domesticus)
by Anastasiya Ivershina, Yuliya Silyukova, Elena Fedorova, Olga Stanishevskaya, Irina Mirzakaeva and Marina Pozovnikova
Animals 2026, 16(2), 225; https://doi.org/10.3390/ani16020225 - 12 Jan 2026
Viewed by 205
Abstract
The study of the relationship between testicular morphology and sperm quality is a pressing issue, for which molecular genetic approaches, including quantitative analysis of gene expression, are being implemented. The aim of this study was to identify correlations between the histomorphological structure of [...] Read more.
The study of the relationship between testicular morphology and sperm quality is a pressing issue, for which molecular genetic approaches, including quantitative analysis of gene expression, are being implemented. The aim of this study was to identify correlations between the histomorphological structure of the testes, fresh sperm parameters, and the expression level of key spermatogenesis genes—TGFB2 and DMRT1—in roosters. The experiment was conducted on 10 Russian Snow White roosters aged 28–32 weeks. Sperm quality was assessed by volume, sperm concentration, total and progressive motility, and viability; histological analysis of the rooster testes was performed. The relative expression of the TGFB2 and DMRT1 genes in sperm was analyzed. Multiple correlation analysis of the data was conducted. A positive correlation was found between ejaculate volume and the number of spermatogonia (p = +0.651), a negative correlation between ejaculate volume and the number of second-order spermatocytes (p = −0.704), a negative correlation between the total cross-sectional area of the seminiferous tubules of the testes and sperm viability (p = −0.782), a negative correlation between the number of seminiferous tubules and the average diameter of their cross-section (p = −0.685), and a positive correlation between total and progressive sperm motility (p = +0.794). Analysis of TGFB2 and DMRT1 gene expression in sperm demonstrated a certain relationship between molecular genetic mechanisms and histomorphometric parameters. The expression level of the DMRT1 gene, which plays a key role in sex determination in birds during embryogenesis, had a number of negative correlations with such parameters as testicle weight (r = −0.782), total/progressive sperm motility (r = −0.552; r = −0.612), and viability (r = −0.552). Expression of the TGFB2 gene had no significant relationship with the studied parameters, but correlation analysis revealed a moderate positive relationship (r = +0.321) with DMRT1 gene expression. The data obtained indicate the expediency of integrating morphometric, cellular, and molecular analysis for an objective assessment of rooster reproductive function. Full article
(This article belongs to the Special Issue Male Germ Cell Development in Animals)
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17 pages, 1829 KB  
Article
Plasma Mucin-1 as a Potential Biomarker for Diabetic Peripheral Neuropathy in Type 2 Diabetes
by Jae-Hyung Park, Thi Nhi Nguyen, Hye Min Shim, Gyeong Im Yu, Junho Kang, Eun Yeong Ha and Hochan Cho
Biomolecules 2026, 16(1), 128; https://doi.org/10.3390/biom16010128 - 12 Jan 2026
Viewed by 145
Abstract
Background: Diabetic peripheral neuropathy (DPN) is a major complication of type 2 diabetes mellitus (T2D) that reduces quality of life and increases the risk of foot ulcers and amputations. Early detection is essential, and blood-based biomarkers may support improved screening and timely intervention. [...] Read more.
Background: Diabetic peripheral neuropathy (DPN) is a major complication of type 2 diabetes mellitus (T2D) that reduces quality of life and increases the risk of foot ulcers and amputations. Early detection is essential, and blood-based biomarkers may support improved screening and timely intervention. This study aimed to identify novel circulating biomarkers for the identification of DPN in patients with T2D. Methods: In the screening phase, plasma samples from 43 participants (10 healthy volunteers [HV], 20 T2D without complications, and 13 T2D with DPN) were analyzed using an antibody array targeting 310 proteins. Thirteen differentially expressed proteins were identified, and six hub proteins were selected through bioinformatic analysis. In the validation phase, plasma concentrations of the six proteins were measured by ELISA in 252 subjects (100 HV, 97 T2D without complications, and 55 T2D with DPN). Mucin-1 expression in sciatic nerves was further evaluated in db/db mice. Results: Of the six hub proteins (TGFB1, MUC1, PF4, IL2RA, SELL, B2M), only mucin-1 showed a significant increase in the DPN group. Plasma mucin-1 positively correlated with MNSI scores and negatively with motor and sensory nerve conduction velocities. In db/db mice, sciatic nerve mucin-1 expression was elevated, while CD31 expression was reduced. Conclusions: Plasma mucin-1 is strongly associated with DPN in both humans and animals and may serve as a promising biomarker for the screening and early identification of DPN. Full article
(This article belongs to the Special Issue Biomarkers in Metabolic Diseases, 2nd Edition)
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14 pages, 1406 KB  
Article
DOTAP-Based Hybrid Nanostructured Lipid Carriers for CRISPR–Cas9 RNP Delivery Targeting TGFB1 in Diabetic Nephropathy
by Nurul Jummah, Hanifa Syifa Kamila, Satrialdi, Aluicia Anita Artarini, Ebrahim Sadaqa, Anindyajati and Diky Mudhakir
Pharmaceutics 2026, 18(1), 94; https://doi.org/10.3390/pharmaceutics18010094 - 11 Jan 2026
Viewed by 220
Abstract
Background: Diabetic nephropathy (DN) is largely driven by transforming growth factor-β1 (TGF-β1)-mediated fibrosis. Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) ribonucleoprotein (RNP) complexes offer precise gene disruption, yet effective non-viral delivery remains a challenge. This study developed cationic lipid-based [...] Read more.
Background: Diabetic nephropathy (DN) is largely driven by transforming growth factor-β1 (TGF-β1)-mediated fibrosis. Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) ribonucleoprotein (RNP) complexes offer precise gene disruption, yet effective non-viral delivery remains a challenge. This study developed cationic lipid-based hybrid nanostructured lipid carriers (NLCs) for intracellular delivery of TGFB1-targeting RNP as an early-stage platform for DN gene modulation. Methods: A single-guide RNA (sgRNA) targeting human TGFB1 was assembled with Cas9 protein (1:1 and 1:2 molar ratios). Hybrid NLCs comprising squalene, glyceryl trimyristate, and the cationic lipid 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) were formulated via optimized emulsification–sonication to achieve sub-100 nm particles. Physicochemical properties, including polydispersity index (PDI), were assessed via dynamic light scattering (DLS), while silencing efficacy in HEK293T cells was quantified using quantitative reverse transcription PCR (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA). Results: Optimized NLCs achieved hydrodynamic diameters of 65–99 nm (PDI < 0.5) with successful RNP complexation. The 1:2 Cas9:sgRNA formulation produced the strongest gene-editing response, reducing TGFB1 mRNA by 67% (p < 0.01) compared with 39% for the 1:1 ratio. This translated to a significant reduction in TGF-β1 protein (p < 0.05) within 24 h. Conclusions: DOTAP-based hybrid NLCs enable efficient delivery of CRISPR–Cas9 RNP and achieve significant suppression of TGFB1 expression at both transcriptional and protein levels. These findings establish a promising non-viral platform for upstream modulation of profibrotic signaling in DN and support further evaluation in kidney-derived cells and in vivo renal models. Full article
(This article belongs to the Topic Advanced Nanocarriers for Targeted Drug and Gene Delivery)
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15 pages, 3280 KB  
Article
Identification and Functional Analysis of tgfb2b Gene in Ovarian Development of Chinese Tongue Sole (Cynoglossus semilaevis)
by Xihong Li, Kaili Zhang, Yue Zhang, Zhijie Li, Zhangfan Chen, Hongyan Wang, Songlin Chen and Na Wang
Biomolecules 2026, 16(1), 105; https://doi.org/10.3390/biom16010105 - 7 Jan 2026
Viewed by 319
Abstract
Transforming growth factor β (TGF-β) superfamily members are critical in teleost sex determination and differentiation. Tgfb2b is an important TGF-β ligand gene exhibiting dominant expression in the ovary of Chinese tongue sole (Cynoglossus semilaevis), yet its function in sex regulation remains [...] Read more.
Transforming growth factor β (TGF-β) superfamily members are critical in teleost sex determination and differentiation. Tgfb2b is an important TGF-β ligand gene exhibiting dominant expression in the ovary of Chinese tongue sole (Cynoglossus semilaevis), yet its function in sex regulation remains unclear. In the present study, the gene expression pattern, transcriptional regulation, and knockdown effect were examined. Its expression persisted and showed a gradual increase throughout ovarian development from 3 months to 1.5 years post-hatching. In situ hybridization (ISH) revealed that the gene was distributed across oocytes at stages I–III, while scarcely detectable in the testis. The transcriptional factors CCAAT/enhancer binding protein α (C/EBPα) and Jun proto-oncogene AP-1 transcription factor subunit (c-Jun) could repress the activity of tgfb2b promoter. In vitro knockdown of tgfb2b in C. semilaevis ovarian cells led to downregulation of its downstream genes (e.g., smad1 and smad2) as well as other sex-related genes (e.g., foxl2 and esr2b). Moreover, multi-omics analysis indicated that, in C. semilaevis gonads, a miRNA named novel-m0083-3p showed an opposite expression pattern with tgfb2b and might have a binding site with the gene. By dual-luciferase assay, tgfb2b was validated to be directly targeted and suppressed by the miRNA. These results demonstrate that tgfb2b plays a significant role in ovarian differentiation and development. Further functional and molecular studies on the interplay between tgfb2b and the foxl2–cyp19a–esr axis will help elucidate the regulatory network underlying sex development in teleost. Full article
(This article belongs to the Section Molecular Genetics)
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12 pages, 2548 KB  
Article
Effects of TGFBR1 on Proliferation of Dermal Papilla Cells in Fine-Wool Sheep
by Tong Xiao, Yu Luo, Chao Yuan, Yufang Song, Jianxiang Tang, Zengkui Lu, Jianbin Liu and Tingting Guo
Animals 2026, 16(1), 36; https://doi.org/10.3390/ani16010036 - 23 Dec 2025
Viewed by 279
Abstract
Dermal papilla cells (DPCs) serve as the signaling hub regulating hair follicle (HF) development and cyclical growth. This study aims to investigate the biological function and molecular mechanisms of TGFBR1 (transforming growth factor β receptor 1), a differentially expressed gene identified through single-cell [...] Read more.
Dermal papilla cells (DPCs) serve as the signaling hub regulating hair follicle (HF) development and cyclical growth. This study aims to investigate the biological function and molecular mechanisms of TGFBR1 (transforming growth factor β receptor 1), a differentially expressed gene identified through single-cell transcriptomic sequencing (scRNA-seq) in the DPCs from fine-wool sheep. Primary DPCs were isolated and purified using a combination of enzymatic digestion and mechanical dissociation, followed by immunofluorescence identification (α-SMA and SOX2-positive). Following successful transfection with constructed TGFBR1 overexpression plasmids and siRNA interference vectors, cell proliferation was assessed via EDU staining and CCK-8 assays. mRNA expression of key genes in Wnt/β-catenin, BMP, and Notch signaling pathways (PCNA, CCND1, CTNNB1, SFRP2, BMP2, NOTCH3, SMAD4, etc.) was validated by RT-qPCR. Single-cell transcriptomics revealed significant downregulation of TGFBR1 in DPCs from fine-wool sheep. Functional validation demonstrated that TGFBR1 overexpression markedly suppressed DPC proliferation, whereas knockdown of TGFBR1 expression promoted DPC proliferation. Molecular mechanism studies showed that TGFBR1 overexpression significantly downregulated PCNA, CCND1, CTNNB1, NOTCH3, and SMAD4 while upregulating SFRP2, BMP2, and TGFB1 expression. These findings demonstrate that TGFBR1 acts as a negative regulator of DPCs proliferation by modulating the activity of multiple signaling pathways, including Wnt/β-catenin, BMP, and Notch, thereby suppressing the proliferative capacity of DPCs. This study not only provides new theoretical support for elucidating the role of the TGF-β signaling pathway in H development but also offers theoretical reference for in-depth research on molecular breeding in ultra -fine-wool sheep and the molecular mechanisms underlying HF development. Full article
(This article belongs to the Section Small Ruminants)
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24 pages, 4082 KB  
Article
Agrimonia pilosa Extract Alleviates CDAHFD-Induced Non-Alcoholic Steatohepatitis and Fibrosis in Mice
by Min-Jeong Jo, Sun Jin Hwang, Myung-Gi Seo, Jun-Ho Lee, Jae Woo Lee, Yoon Hee Kim, Yongduk Kim and Sang-Joon Park
Nutrients 2026, 18(1), 42; https://doi.org/10.3390/nu18010042 - 22 Dec 2025
Viewed by 474
Abstract
Background: Non-alcoholic steatohepatitis (NASH) lacks approved pharmacotherapies despite affecting approximately 25% of the global population. Agrimonia pilosa, a traditional herb with anti-inflammatory and antioxidant properties, remains unexplored for NASH treatment. Objective: This study investigated the hepatoprotective effects and mechanisms of Agrimonia pilosa [...] Read more.
Background: Non-alcoholic steatohepatitis (NASH) lacks approved pharmacotherapies despite affecting approximately 25% of the global population. Agrimonia pilosa, a traditional herb with anti-inflammatory and antioxidant properties, remains unexplored for NASH treatment. Objective: This study investigated the hepatoprotective effects and mechanisms of Agrimonia pilosa extract (APE) in NASH models. Methods: HepG2 cells were treated with free fatty acids (0.125 mM) and APE (+12.5–50 μg/mL). C57BL/6J mice received a choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD) for 12 weeks with APE (25–100 mg/kg/day), silymarin (100 mg/kg/day), or luteolin (20 mg/kg/day). Lipid accumulation, liver enzymes, histopathology, and molecular markers were assessed. Results: APE dose-dependently reduced lipid accumulation in FFA-treated cells, suppressed lipogenic factors (SREBF1, CEBPA, and PPARG), and upregulated fatty acid oxidation enzymes (CPT1A and PPARA) via AMPK/SIRT1 activation. In NASH mice, APE (100 mg/kg) significantly decreased serum ALT (160.0 ± 49.1 vs. 311.2 ± 66.7 U/L) and AST (96.0 ± 18.7 vs. 219.0 ± 55.7 U/L, p < 0.001), reduced hepatic macrophage infiltration by 68%, and substantially attenuated inflammatory markers (Ccl2, Tnf, and IL6), oxidative stress indicators (NRF2, HMOX1, and CYBB), and fibrogenic markers (ACTA2, COL1A1, and TGFB1) by 83–85% (p < 0.001). Collagen deposition decreased from 5.63 ± 0.39% to 1.54 ± 0.03% (p < 0.001). Conclusions: APE exerts potent hepatoprotective effects through multi-targeted modulation of lipid metabolism, inflammation, oxidative stress, and fibrosis via AMPK/SIRT1 pathway activation, supporting its potential as a natural therapeutic intervention for NASH. Full article
(This article belongs to the Special Issue Nutrition Therapy for Liver and Associated Metabolic Diseases)
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19 pages, 6236 KB  
Article
Sequential Inflammatory and Matrisome Programs Drive Remodeling of the Mouse Carotid–Jugular Arteriovenous Fistula
by Filipe F. Stoyell-Conti, Alexander M. Kaiser, Miguel G. Rojas, Yuntao Wei, Matthew S. Sussman, Juan S. Lopez-McCormick, Marwan Tabbara, Xiaofeng Yang, Roberto I. Vazquez-Padron and Laisel Martinez
Cells 2025, 14(24), 1998; https://doi.org/10.3390/cells14241998 - 16 Dec 2025
Viewed by 587
Abstract
The mouse carotid–jugular arteriovenous fistula (AVF) is a widely adopted surgical model to study venous remodeling after AVF creation. Despite its increasing use, the extent to which this model recapitulates the cellular and molecular remodeling processes observed in humans remains uncertain, which is [...] Read more.
The mouse carotid–jugular arteriovenous fistula (AVF) is a widely adopted surgical model to study venous remodeling after AVF creation. Despite its increasing use, the extent to which this model recapitulates the cellular and molecular remodeling processes observed in humans remains uncertain, which is essential for validating its translational relevance. Using bulk and single-cell RNA sequencing, we have depicted the transcriptional and cellular evolution of the mouse jugular vein after AVF anastomosis. Global transcriptomic profiling revealed that venous remodeling begins with a robust inflammatory response, followed by a prominent extracellular matrix (ECM) remodeling phase that peaks at postoperative day 10. Single-cell analyses confirmed the role of macrophage (3-fold) and neutrophil infiltration (12-fold) in sustaining the onset of venous remodeling. These monocytes/macrophages exhibited marked upregulation of pro-inflammatory and pro-fibrotic genes, including Il1b, Spp1, Fn1, Thbs1, and Tgfb1. Evidence of the differentiation of fibroblasts into myofibroblasts positive for Postn, Col8a1, and Thbs1 emerged by postoperative day 5. The temporal dynamics of differentially expressed genes in these myofibroblasts closely mirrored the ECM gene expression patterns identified by bulk RNA-seq, indicating that they are the principal source of ECM deposition in the AVF. Cell-to-cell communication analyses highlighted macrophages and fibroblasts as the main populations driving postoperative remodeling. Comparative analysis with single-cell data from human pre-access veins and AVFs demonstrated that the mouse model reproduces the core inflammatory–fibrotic axis of fibroblast activation observed in humans, supporting its utility for mechanistic studies of postoperative ECM remodeling. Full article
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18 pages, 3071 KB  
Article
Bulk RNA Sequencing Reveals Signature Differences in Key Cell Signaling Pathways Between Porcine Venous and Arterial Smooth Muscle Cells
by Kent A. Lee, Wei Li, Unimunkh Uriyanghai, Christine Wai, Huanjuan Su, Anthony Yang, Lianxia Li, Vinay A. Sudarsanam, John S. Poulton, Prabir Roy-Chaudhury and Gang Xi
Int. J. Mol. Sci. 2025, 26(24), 11948; https://doi.org/10.3390/ijms262411948 - 11 Dec 2025
Viewed by 379
Abstract
We recently identified significant differences between porcine arterial and venous smooth muscle cells (ApSMCs and VpSMCs) in the expression of numerous genes and activity of several important signaling pathways. To understand the mechanisms that are responsible for these differences, we performed a genome-wide [...] Read more.
We recently identified significant differences between porcine arterial and venous smooth muscle cells (ApSMCs and VpSMCs) in the expression of numerous genes and activity of several important signaling pathways. To understand the mechanisms that are responsible for these differences, we performed a genome-wide comparison of VpSMCs and ApSMCs using bulk RNA sequencing. A principal component analysis (PCA) plot and heatmaps revealed a clear separation of the two groups of samples. Using a standard cutoff (≥2-fold change, false discovery rate (FDR) ≤ 0.05), 466 genes were highly expressed in ApSMCs, and 358 genes were highly expressed in VpSMCs. Functional pathway analyses were conducted using the Gene Set Enrichment Analysis (GSEA) tool. The top 15 enriched pathways of the GSEA and Overrepresentation Analysis (ORA) results were detected by comparing the dataset against the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO) biological process, GO cellular component, GO molecular function, and WikiPathways databases. Both the GSEA and ORA results revealed that the top enriched pathways are mostly linked to cell cycle, cell structure, and cell differentiation. Further analysis of differentially expressed genes (DEGs) in a specific pathway identified that different sets of genes were utilized to regulate the same pathway between ApSMCs and VpSMCs. For example, in the cell cycle pathway, TGFB1, GADD45A, and TP53 were expressed highly in ApSMCs, while SKP2, PCK1, CDK1, and PPP2CA were expressed highly in VpSMCs. This study identified key differences in the gene expression patterns of two subsets of VSMCs and found that different sets of genes are utilized in specific signaling pathways within the different subtypes of cells, which provides crucial information for developing vein- or artery-specific strategies to prevent corresponding vascular diseases. Full article
(This article belongs to the Section Molecular Biology)
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29 pages, 3286 KB  
Article
Bioinformatic Approach to Identify Potential TGFB2-Dependent and Independent Prognostic Biomarkers for Ovarian Cancers Treated with Taxol
by Sanjive Qazi, Stephen Richardson, Mike Potts, Scott Myers, Saran Saund, Tapas De and Vuong Trieu
Int. J. Mol. Sci. 2025, 26(24), 11900; https://doi.org/10.3390/ijms262411900 - 10 Dec 2025
Viewed by 492
Abstract
High-grade serous ovarian carcinoma is the most common and aggressive form of ovarian cancer, accounting for over 60% of cases and nearly 75% of deaths, mainly due to late diagnosis and tumor aggressiveness. Standard treatment is platinum-based chemotherapy with paclitaxel, but relapse is [...] Read more.
High-grade serous ovarian carcinoma is the most common and aggressive form of ovarian cancer, accounting for over 60% of cases and nearly 75% of deaths, mainly due to late diagnosis and tumor aggressiveness. Standard treatment is platinum-based chemotherapy with paclitaxel, but relapse is frequent. This study aimed to identify prognostic biomarkers for patients with poor survival outcomes after Taxol treatment using bioinformatics analysis. We examined the effects of TGFB2 mRNA expression and other markers on overall survival in serous ovarian cancer using the TCGA database, applying a multivariate Cox model that included interaction terms to identify TGFB2-dependent and independent prognostic markers, and controlling for age and treatment type. Candidate TGFB2-independent prognostic markers from TCGA were further validated using patient data from the KMplotter database. High TGFB2 mRNA expression emerged as a prognostic biomarker for three potential gene targets (TRPV4, STAU2, and HOXC4) associated with improved OS at low levels of gene target expression, we identified four additional markers (CLIC3, ANPEP/LAP1, RIN2, and EMP1) that exhibited a TGFB2-independent negative correlation between mRNA expression and OS across the full spectrum of gene expression values in the ovarian cancer cohort validated using independent dataset from KMplotter, for Taxol-treated ovarian cancer patients. This study proposes a panel of potential prognostic biomarkers for the treatment of ovarian cancer patients, particularly by leveraging TGFB2-dependent mRNA expression as a significant biomarker, alongside four additional TGFB2-independent prognostic markers, for patients undergoing Taxol-based therapies. Future prospective clinical trials will be required to validate these prognostic markers. Full article
(This article belongs to the Special Issue Molecular Biomarkers for Targeted Therapies)
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21 pages, 3476 KB  
Article
Multi-Level Profiling of MAPK-Associated Genes and MicroRNAs Uncovers Regulatory Networks in Breast Cancer Subtypes
by Katarzyna Król-Jatręga, Elżbieta Mitka-Krysiak, Kacper Boroń, Piotr Ossowski, Nikola Zmarzły, Paweł Ordon, Wojciech Kulej, Tomasz Sirek, Agata Sirek, Dariusz Boroń, Grzegorz Wyrobiec, Yuriy Prudnikov and Beniamin Oskar Grabarek
Int. J. Mol. Sci. 2025, 26(24), 11831; https://doi.org/10.3390/ijms262411831 - 7 Dec 2025
Viewed by 568
Abstract
Breast cancer (BC) comprises heterogeneous subtypes with distinct molecular drivers and clinical behaviors. Among the key signaling pathways implicated in BC progression is the mitogen-activated protein kinase (MAPK) cascade, which regulates cell proliferation, apoptosis, and stress responses. microRNAs (miRNAs), as post-transcriptional regulators, are [...] Read more.
Breast cancer (BC) comprises heterogeneous subtypes with distinct molecular drivers and clinical behaviors. Among the key signaling pathways implicated in BC progression is the mitogen-activated protein kinase (MAPK) cascade, which regulates cell proliferation, apoptosis, and stress responses. microRNAs (miRNAs), as post-transcriptional regulators, are increasingly recognized as modulators of MAPK-associated genes, yet their integrated role across BC subtypes remains incompletely understood. This study included 405 patients with histopathologically confirmed BC, stratified into luminal A (LumA), HER2-negative luminal B, HER2-positive luminal B, non-luminal HER2-positive, and triple-negative breast cancer (TNBC). Control tissues were obtained from matched surgical margins. We performed mRNA profiling (Affymetrix microarrays), reverse transcription-quantitative polymerase chain reaction (RT-qPCR), protein quantification (enzyme-linked immunosorbent assay (ELISA), and miRNA expression analysis. Predicted miRNA-mRNA interactions were analyzed using the miRDB database. Functional protein–protein interactions were explored using the STRING database. MAP3K1, MAP2K4, and TP53 were significantly downregulated across all subtypes, while PPM1D, LMTK3, and TGFB1 were upregulated, especially in TNBC. These alterations were supported by concordant changes at the protein level. Dysregulated miRNAs—miR-21-3p, miR-23c, miR-27a-3p, miR-205-3p, and miR-300—exhibited in-verse expression patterns relative to their predicted target genes. STRING analysis identified TP53 as a central hub, linking MAPK signaling with stress and apoptotic pathways. This integrated transcriptomic and miRNA profiling study reveals subtype-specific dysregulation of MAPK-associated genes and their miRNA regulators in BC, with TNBC exhibiting the most profound alterations. These findings provide insight into potential targets for personalized therapeutic strategies. Full article
(This article belongs to the Special Issue Breast Cancer: From Pathophysiology to Novel Therapies)
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21 pages, 7902 KB  
Article
Innovative In Vivo Imaging and Single Cell Expression from Tumor Bulk and Corpus Callosum Reveal Glioma Stem Cells with Unique Regulatory Programs
by Natalia dos Santos, Aline Aquino, Friedrich Preußer, Fabio Rojas Rusak, Elisa Helena Farias Jandrey, Miyuki Uno, Tatiane Katsue Furuya, Carmen Lucia Penteado Lancellotti, Marcos Vinicius Calfat Maldaun, Roger Chammas, Stephan Preibisch, Anamaria Aranha Camargo, Cibele Masotti and Erico Tosoni Costa
Cancers 2025, 17(23), 3851; https://doi.org/10.3390/cancers17233851 - 30 Nov 2025
Cited by 1 | Viewed by 618
Abstract
Background/Objectives: High-grade gliomas (HGGs), including glioblastomas, are among the most aggressive brain tumors due to their high intratumoral heterogeneity and extensive infiltration. Glioma stem-like cells (GSCs) frequently invade along white matter tracts such as the corpus callosum, but the molecular programs driving [...] Read more.
Background/Objectives: High-grade gliomas (HGGs), including glioblastomas, are among the most aggressive brain tumors due to their high intratumoral heterogeneity and extensive infiltration. Glioma stem-like cells (GSCs) frequently invade along white matter tracts such as the corpus callosum, but the molecular programs driving this region-specific invasion remain poorly defined. The aim of this study was to identify transcriptional signatures associated with GSC infiltration into the corpus callosum. Methods: We established an orthotopic xenograft model by implanting fluorescently labeled human GSCs into nude mouse brains. Tumor growth and invasion patterns were assessed using tissue clearing, light-sheet fluorescence microscopy, and histological analyses. To characterize region-specific molecular profiles, we performed microfluidic-based single-cell RNA expression analysis of 48 invasion- and stemness-related genes in cells isolated from the tumor bulk (TB) and corpus callosum (CC). Results: By six weeks post-implantation, GSCs displayed marked tropism for the corpus callosum, with distinct infiltration patterns captured by three-dimensional imaging. Single-cell gene expression profiling revealed significant differences in 7 of the 48 genes (14.6%) between TB- and CC-derived GSCs. These genes—NES, CCND1, GUSB, NOTCH1, E2F1, EGFR, and TGFB1—collectively defined a “corpus callosum invasion signature” (CC-Iv). CC-derived cells showed a unimodal, high-expression profile of CC-Iv genes, whereas TB cells exhibited bimodal distributions, suggesting heterogeneous transcriptional states. Importantly, higher CC-Iv expression correlated with worse survival in patients with low-grade gliomas. Conclusions: This multimodal approach identified a corpus callosum-specific invasion signature in glioma stem-like cells, revealing how local microenvironmental cues shape transcriptional reprogramming during infiltration. These findings provide new insights into the spatial heterogeneity of gliomas and highlight potential molecular targets for therapies designed to limit tumor spread through white matter tracts. Full article
(This article belongs to the Section Molecular Cancer Biology)
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30 pages, 4746 KB  
Article
Bioinformatic Approach to Identify Positive Prognostic TGFB2-Dependent and Negative Prognostic TGFB2-Independent Biomarkers for Breast Cancers
by Sanjive Qazi, Stephen Richardson, Mike Potts, Scott Myers and Vuong Trieu
Int. J. Mol. Sci. 2025, 26(23), 11580; https://doi.org/10.3390/ijms262311580 - 29 Nov 2025
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Abstract
Breast cancer is highly heterogeneous, with multiple subtypes that differ in molecular and clinical characteristics. It remains the most common cancer among women worldwide. We conducted a hypothesis-generating study using a bioinformatics approach in order to identify potential prognostic biomarkers for breast cancer [...] Read more.
Breast cancer is highly heterogeneous, with multiple subtypes that differ in molecular and clinical characteristics. It remains the most common cancer among women worldwide. We conducted a hypothesis-generating study using a bioinformatics approach in order to identify potential prognostic biomarkers for breast cancer patients across multiple molecular subtypes. Given the influential role of the transforming growth factor beta (TGFB) pathway in shaping the immune microenvironment, we focused on the isoform, transforming growth factor beta 2 (TGFB2), which is upregulated in tumors, to identify TGFB2-dependent and -independent biomarkers for breast cancer patients’ overall survival (OS) responses. We evaluated the impact of TGFB2 mRNA expression, in conjunction with other potential prognostic markers, on overall survival (OS) in breast cancer patients using The Cancer Genome Atlas (TCGA) and KMplotter databases. We employed a multivariate Cox proportional hazards model to compute hazard ratios (HRs) for TGFB2 mRNA expression, integrating an interaction term that accounts for the multiplicative relationship between TGFB2 and marker gene expressions while controlling age at diagnosis and cancer subtype and differentiating between patients receiving chemotherapy alone and those undergoing alternative therapeutic interventions. We used the KMplotter database to confirm TGFB2-independent prognostic markers from TCGA data. In cases dependent on TGFB2, increased mRNA expression of TGFB2 alongside higher levels of GDAP1, TBL1XR1, RNFT1, HACL1, SLC27A2, NLE1, or TXNDC16 was correlated with improved OS among breast cancer patients, of which four genes were upregulated in tumor tissues (SLC27A2, TXNDC16, TBL1XR1, GDAP1). Future studies will be required to confirm breast cancer patients could improve OS outcomes for patients expressing high levels of TGFB2 and the marker genes in prospective clinical trials. Additionally, multivariate analysis revealed that the elevated expression of six genes (ENO1, GLRX2, PLOD1, PRDX4, TAGLN2, TMED9) were correlated with increases in HR, independent of TGFB2 mRNA expression; all except GLRX2 were identified as druggable targets. Future investigations assessing protein expression in breast cancer tumors to confirm the results of our retrospective analysis of mRNA levels will determine whether the protein products of these genes represent viable therapeutic targets. Protein–protein interaction (STRING) analysis indicated that TGFB2 is associated with EGFR and MYC from the PAM50 breast cancer gene signature. These findings suggest that correlation of TGFB2-related markers could potentially complement the PAM50 signature in the assessment of OS prognosis in breast cancer patients, but further validation of the TGFB2/EGFR/MYC proteins in tumors is warranted. Full article
(This article belongs to the Section Molecular Oncology)
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18 pages, 1301 KB  
Article
Development of a MassARRAY Genotyping Platform and Its Clinical Application for Venous Thromboembolism Risk Assessment in Thai Patients
by Dollapak Apipongrat, Chonlada Laoruangroj, Oytip Nathalang, Pasra Arnutti, Montalee Theeraapisakkun and Wittawat Chantkran
Med. Sci. 2025, 13(4), 282; https://doi.org/10.3390/medsci13040282 - 24 Nov 2025
Viewed by 486
Abstract
Background: Venous thromboembolism (VTE) is a multifactorial disorder influenced by both genetic and environmental factors, with substantial variability in susceptibility across populations. Data on VTE-associated genetic variants in Asian populations, including Thais, remain limited. To address this, we developed a 39-single-nucleotide polymorphism (SNP) [...] Read more.
Background: Venous thromboembolism (VTE) is a multifactorial disorder influenced by both genetic and environmental factors, with substantial variability in susceptibility across populations. Data on VTE-associated genetic variants in Asian populations, including Thais, remain limited. To address this, we developed a 39-single-nucleotide polymorphism (SNP) genotyping panel using the MassARRAY platform and evaluated its association with VTE in a Thai cohort. Methods: A total of 209 individuals, comprising 122 patients with objectively confirmed VTE and 87 age- and sex-matched healthy controls, were genotyped. Allele frequencies were compared, and associations with VTE were assessed. Results: Seven SNPs demonstrated significant associations: five risk alleles (PROC rs146922325, ABO rs8176743, FGG rs2066865, F11 rs4253417, and HIVEP1 rs169713) and two protective alleles (F5 rs4524 and TGFB2 rs57615042). To examine cumulative effects, a polygenic risk score (PRS) integrating genetic and clinical factors was constructed. Higher PRS was significantly associated with recurrence, particularly among patients with unprovoked VTE, conferring more than a threefold increase in recurrence risk (HR = 3.53, 95% CI: 1.04–10.2, p = 0.043). These findings provide the first systematic evidence of population-specific genetic risk factors for VTE in Thais and highlight the clinical potential of PRS for recurrence prediction. Conclusions: The MassARRAY-based panel offers a cost-effective, high-throughput strategy for simultaneous SNP detection, supporting scalable genomic studies and personalized risk stratification. Our results contribute to understanding the genetic architecture of VTE and highlight the value of incorporating non-European populations into genetic studies to advance precision medicine. Full article
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