International Journal of Molecular Sciences

16 pages, 3092 KiB

Open AccessFeature PaperArticle

Potential Influence of ADAM9 Genetic Variants and Expression Levels on the EGFR Mutation Status and Disease Progression in Patients with Lung Adenocarcinoma

by Jer-Hwa Chang, Tsung-Ching Lai, Kuo-Hao Ho, Thomas Chang-Yao Tsao, Lun-Ching Chang, Shun-Fa Yang and Ming-Hsien Chien

Int. J. Mol. Sci. 2025, 26(10), 4606; https://doi.org/10.3390/ijms26104606 (registering DOI) - 11 May 2025

Abstract

Lung adenocarcinoma (LUAD) is driven by epidermal growth factor receptor (EGFR) mutations, making it a key therapeutic target. ADAM9, a member of the A disintegrin and metalloproteinase (ADAM) family, facilitates the release of growth factors and was implicated in activating the [...] Read more.

Lung adenocarcinoma (LUAD) is driven by epidermal growth factor receptor (EGFR) mutations, making it a key therapeutic target. ADAM9, a member of the A disintegrin and metalloproteinase (ADAM) family, facilitates the release of growth factors and was implicated in activating the EGFR-mediated progression in several cancer types. In this study, we explored potential associations among ADAM9 single-nucleotide polymorphisms (SNPs), the EGFR mutation status, and the clinicopathological progression of LUAD in a Taiwanese population. In total, 535 LUAD patients with various EGFR statuses were enrolled, and allelic distributions of ADAM9 SNPs—located in promoter and intron regions, including rs78451751 (T/C), rs6474526 (T/G), rs7006414 (T/C), and rs10105311 (C/T)—were analyzed using a TaqMan allelic discrimination assay. We found that LUAD patients with at least one polymorphic G allele in ADAM9 rs6474526 had a lower risk of developing EGFR mutations compared to those with the wild-type (WT) TT genotype. Furthermore, G-allele carriers (TG + GG) of rs6474526 were associated with an increased likelihood of developing larger tumors (T3 or T4), particularly among patients with mutant EGFR. Conversely, in patients with WT EGFR, carriers of the T allele in rs10105311 had a lower risk of progressing to advanced stages (stage III or IV). Among females or non-smokers, G-allele carriers of rs6474526 demonstrated a higher risk of advanced tumor stages and distant metastases. In clinical data from the Genotype-Tissue Expression (GTEx) database, individuals with the polymorphic T allele in rs6474526 showed reduced ADAM9 expression in lung and whole blood tissues. Screening the genotype of rs6474526 in a set of LUAD cell lines revealed that cells carrying at least one minor G allele exhibited higher ADAM9 levels compared to those with the TT genotype. Additionally, analyses using TCGA and CPTAC databases revealed elevated ADAM9 expression in LUAD specimens compared to normal tissues. Elevated protein levels were correlated with advanced T stages, pathological stages, and worse prognoses. In summary, our results suggest that ADAM9 genetic variants of rs6474526 may affect ADAM9 expression and are associated with the EGFR mutation status. Both rs6474526 and rs10105311 were correlated with disease progression in LUAD patients. These variants could serve as potential biomarkers for predicting clinical outcomes. Full article

(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)

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18 pages, 3829 KiB

Open AccessArticle

Integrative ATAC-Seq and RNA-Seq Analysis Reveals Key Transcription Factors Mediating Low Salinity Adaptation in Penaeid Shrimp

by Chuntao Zhang, Jianbo Yuan, Roujing Li, Zhanyuan Yang, Man Luo, Xiaoyun Zhong, Jie Hu, Shuqing Si, Xiaojun Zhang and Fuhua Li

Int. J. Mol. Sci. 2025, 26(10), 4605; https://doi.org/10.3390/ijms26104605 (registering DOI) - 11 May 2025

Abstract

Salinity serves as an important environmental factor in ecosystems, driving the evolution of adaptive strategies in euryhaline species. The Pacific white shrimp, Litopenaeus vannamei, is a representative euryhaline species. However, the molecular mechanisms, particularly the roles of cis-regulatory elements, remain elusive in [...] Read more.

Salinity serves as an important environmental factor in ecosystems, driving the evolution of adaptive strategies in euryhaline species. The Pacific white shrimp, Litopenaeus vannamei, is a representative euryhaline species. However, the molecular mechanisms, particularly the roles of cis-regulatory elements, remain elusive in penaeid shrimp. This study tackles this gap by subjecting L. vannamei to a gradual reduction in salinity from 30‰ to 3‰, and then applying ATAC-seq and RNA-seq techniques to dissect the cis-regulation mechanisms underlying low salinity adaptation. A key finding reveals a positive correlation between chromatin accessibility and gene expression, with 36.8% of differentially expressed genes directly associated with changes in chromatin accessibility. The cis-regulation of many osmoregulation-related pathways, such as betaine synthesis and PI3K-Akt signaling pathways, appeared to be a crucial strategy for salinity adaptation in shrimp. By analyzing differentially accessible regions under low salinity stress, we uncovered two known and seven novel candidate transcription factors (TFs) that may play pivotal roles in salinity adaptation. We further conducted a comprehensive analysis of these TFs, including their functions, expression profiles, consensus TFBS motifs, and the functional enrichment and expression profiles of their targeted genes. This study elucidates a complex cis-regulatory network that enables exceptional salinity tolerance in L. vannamei, which provides a foundation for the refinement of genetic breeding programs and desalination aquaculture for penaeid shrimp. Full article

(This article belongs to the Special Issue New Molecular Perspectives in Crustacean Neuroendocrinology)

25 pages, 20577 KiB

Open AccessArticle

Zebrafish cdh23 Affects Rod Cell Phototransduction Through Regulating Ca²⁺ Transport and MAPK Signaling Pathway

by Xiaoying Zheng, Binling Xie, Dingrui Chen, Jifan Jiang, Ting Zeng, Lei Xiong, Qingying Shi, Hao Xie, Yisheng Cai, Jiaxin Liang, Song Chen, Xiaochao Qu and Huaping Xie

Int. J. Mol. Sci. 2025, 26(10), 4604; https://doi.org/10.3390/ijms26104604 (registering DOI) - 11 May 2025

Abstract

Mutations in the pathogenic gene CDH23 are known to cause Usher syndrome, affecting both auditory and visual functions. Our previous results provided valuable insights into the mechanisms underlying congenital hearing loss associated with CDH23 mutations. However, the molecular mechanisms and signaling pathways that [...] Read more.

Mutations in the pathogenic gene CDH23 are known to cause Usher syndrome, affecting both auditory and visual functions. Our previous results provided valuable insights into the mechanisms underlying congenital hearing loss associated with CDH23 mutations. However, the molecular mechanisms and signaling pathways that influence vision remain largely unknown. In this study, transcriptional sequencing and bioinformatics analysis were conducted to compare gene expression between the control and cdh23^−/⁻. Additionally, RT-qPCR experiments were performed to further validate the bioinformatics analysis results. The comparative transcriptomic analysis identified differentially expressed genes associated with photoreceptor degeneration and the mitogen-activated protein kinase (MAPK) signaling pathway. Embryos were subjected to hematoxylin and eosin (H&E) staining to assess their histological changes. The results showed that the cdh23^−/− retina was morphologically indistinguishable from the control. Apoptosis was assessed using TUNEL staining, which revealed an increase in total cell death in the cdh23^−/⁻ retina. Our results revealed that the cell death was induced by Ca²⁺ and MAPK signaling interactions following photoreceptor degeneration. This study provides insights into the mechanisms underlying the role of cdh23 in vision. Full article

(This article belongs to the Section Molecular Biology)

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22 pages, 1950 KiB

Open AccessReview

Targeting Mitochondrial Dysfunction to Prevent Endothelial Dysfunction and Atherosclerosis in Diabetes: Focus on the Novel Uncoupler BAM15

by Woong Bi Jang, Vinoth Kumar Rethineswaran and Sang-Mo Kwon

Int. J. Mol. Sci. 2025, 26(10), 4603; https://doi.org/10.3390/ijms26104603 (registering DOI) - 11 May 2025

Abstract

Diabetes mellitus is a chronic metabolic disorder characterized by persistent hyperglycemia, leading to endothelial dysfunction and accelerated atherosclerosis. Mitochondrial dysfunction, oxidative stress, and dysregulated lipid metabolism contribute to endothelial cell (EC) injury, promoting plaque formation and increasing cardiovascular disease risk. Current lipid-lowering therapies [...] Read more.

Diabetes mellitus is a chronic metabolic disorder characterized by persistent hyperglycemia, leading to endothelial dysfunction and accelerated atherosclerosis. Mitochondrial dysfunction, oxidative stress, and dysregulated lipid metabolism contribute to endothelial cell (EC) injury, promoting plaque formation and increasing cardiovascular disease risk. Current lipid-lowering therapies have limited effectiveness in restoring endothelial function, highlighting the need for novel strategies. Mitochondrial uncoupling has emerged as a promising approach, with BAM15—a newly identified mitochondrial uncoupler—showing potential therapeutic benefits. BAM15 enhances fatty acid oxidation (FAO), reduces reactive oxygen species, and protects ECs from hyperglycemia-induced apoptosis. Unlike conventional uncouplers, BAM15 demonstrates improved tolerability and efficacy without severe off-target effects. It restores mitochondrial function, improves endothelial survival, and supports metabolic homeostasis under hyperglycemic conditions. This review uniquely integrates emerging evidence on mitochondrial dysfunction, endothelial metabolism, and FAO to highlight the novel role of BAM15 in restoring vascular function in diabetes. We provide the first focused synthesis of BAM15’s mechanistic impact on EC bioenergetics and position it within the broader landscape of mitochondrial-targeted therapies for diabetic vascular complications. Further research is needed to elucidate the molecular mechanism through which BAM15 modulates EC metabolism and to evaluate its long-term vascular effects in diabetic models. Full article

(This article belongs to the Special Issue Cardiovascular Diseases: From Pathology to Therapeutics)

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20 pages, 4389 KiB

Open AccessArticle

Genome-Wide Identification and Expression Profiling of Phosphatidylethanolamine-Binding Protein (PEBP) Genes in Helianthus annuus L.

by Yiyi Sun, Yanwen Wang, Jingyan Bai, Jiatong Guo, Guiting Li, Qiuzhen Tian, Shuping Lv, Hengchun Cao, Xiaojie Yang and Lingyun Liu

Int. J. Mol. Sci. 2025, 26(10), 4602; https://doi.org/10.3390/ijms26104602 (registering DOI) - 11 May 2025

Abstract

The phosphatidylethanolamine-binding protein (PEBP) gene family is critical for regulating plant growth, development, and flowering. Sunflower (Helianthus annuus L.) is the fourth most important oilseed crop globally. However, the genomic structure and functional diversity of PEBP genes in sunflower remain unexplored. Leveraging [...] Read more.

The phosphatidylethanolamine-binding protein (PEBP) gene family is critical for regulating plant growth, development, and flowering. Sunflower (Helianthus annuus L.) is the fourth most important oilseed crop globally. However, the genomic structure and functional diversity of PEBP genes in sunflower remain unexplored. Leveraging the recently assembled telomere-to-telomere (T2T) sunflower genome, a genome-wide analysis of the HaPEBP family was carried out. A total of 12 PEBP genes were identified in sunflower and categorized into three subfamilies: TFL1-like, FT-like, and MFT-like. Phylogenetic and synteny analyses revealed that tandem duplication events have substantially contributed to the evolution and expansion of the HaPEBP gene family. Furthermore, the analysis of the promoter regions revealed 77 distinct cis-acting elements, including 35 related to light signaling and growth regulation, highlighting their potential involvement in the regulation of flowering and development in sunflower. Expression profile analysis using RNA-seq data across various tissues indicated that FT-like and TFL1-like HaPEBP genes may be the key regulators of flowering time and plant architecture in sunflower varieties. This study offers valuable insights into the structural, evolutional, and functional dynamics of the HaPEBP gene family and holds significant implications for sunflower breeding strategies aimed at optimizing flowering time and plant architecture traits. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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15 pages, 12467 KiB

Open AccessArticle

Deciphering the Transcriptomic Complexity of Yak Skin Across Different Ages and Body Sites

by Xiaolan Zhang, Bingang Shi, Zhidong Zhao, Yunqi Deng, Xuelan Zhou and Jiang Hu

Int. J. Mol. Sci. 2025, 26(10), 4601; https://doi.org/10.3390/ijms26104601 (registering DOI) - 11 May 2025

Abstract

Differences in skin and hair phenotypes between the scapular and ventral regions of yaks (Bos grunniens) are obvious and become more prominent with age. However, the genetic mechanism that causes differences in yak skin at different ages has not been reported. In this [...] Read more.

Differences in skin and hair phenotypes between the scapular and ventral regions of yaks (Bos grunniens) are obvious and become more prominent with age. However, the genetic mechanism that causes differences in yak skin at different ages has not been reported. In this study, we investigated the transcriptomic profile of yak skin across different ages (0.5 years, 2.5 years, and 4.5 years) and body sites (scapular and ventral regions). Differential gene expression analysis was initially conducted to explore the transcriptomic differences in skin at different ages and different body sites. Subsequently, weighted gene co-expression network analysis (WGCNA) was employed to analyze the transcriptomic data comprehensively. The results showed that, among all comparison groups, the Y2.5_S vs. Y2.5_V group (regional comparison) exhibited the highest number of DEGs, with 491 genes (179 upregulated and 312 downregulated), followed by the Y2.5_V vs. Y0.5_V group (age comparison), which had 370 DEGs (103 upregulated and 267 downregulated). DEGs such as IGF2BP3, ADCY8, FOSL1, and S100A8 were found in all comparison groups of different ages, and multiple members of the HOX gene family including HOXC10, HOXA9, HOXA6, HOXB9, and HOXB6 were differentially expressed in comparison groups at different sites. Functional enrichment analysis showed that there were more obvious differences in immune function between different ages of skin and more obvious differences in endocrine function between different parts of skin. WGCNA revealed that genes related with immunity such as GLYATL2, ACSL5, and SPDEF were the core genes of the co-expression module associated with the scapula region, and multiple genes related to hair follicle development such as FOXN1, OVOL1, DLX3, HOXC13, and TCHH were found to be the hub genes of the co-expression module associated with the ventral region. Overall, our study provides valuable insights into the transcriptomic complexity of yak skin across different ages and body sites. The differential gene expression patterns and co-expression network modules identified in this study lay the foundation for further research on skin biology and adaptation mechanisms in yaks. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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14 pages, 1493 KiB

Open AccessArticle

CRISPR/Cas9-Based Modeling of JAK2 V617F Mutation in K562 Cells Reveals Enhanced Proliferation and Sensitivity to Therapeutic Agents

by Nungruthai Nilsri, Rujira Mekchaaum, Supaporn Kalasin, Jirapas Jongjitwimol and Krai Daowtak

Int. J. Mol. Sci. 2025, 26(10), 4600; https://doi.org/10.3390/ijms26104600 (registering DOI) - 11 May 2025

Abstract

The Janus kinase 2 (JAK2) protein fulfills an important role in hematopoiesis via the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway, as it provides the genetic driver of BCR::ABL1-negative myeloproliferative neoplasms (MPNs), which are clinically manifested as polycythemia vera (PV), [...] Read more.

The Janus kinase 2 (JAK2) protein fulfills an important role in hematopoiesis via the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway, as it provides the genetic driver of BCR::ABL1-negative myeloproliferative neoplasms (MPNs), which are clinically manifested as polycythemia vera (PV), essential thrombocythemia (ET), and primary myelofibrosis (PMF). The most common cause of MPNs is the mutation of JAK2 V617F in the JAK2 gene, which results in increased cell proliferation. However, both the pathogenesis and treatment regimen of BCR::ABL1-negative MPNs remain poorly understood. The aim of the present study was to establish K562 cell lines with a point mutation in exon 14 (JAK2p.V617F) using CRISPR/Cas9 technology. The modified JAK2 V617F cell lines were examined for the gene mutation using droplet digital PCR (DDPCR), and the presence of the mutation was confirmed by DNA sequencing. Modified cells were characterized by measuring JAK2 gene expression and the extent of cell proliferation. Interferon α2a (IFN-α2a) and arsenic trioxide were also administered to the cells to explore their potential effects. The JAK2 V617F-mutated cells were found to exhibit a higher level of JAK2 gene expression compared with the wild type. Interestingly, a significant increase in the proliferation rate was observed with the modified cells compared with the wild type cells (p < 0.001), as assessed from the JAK2 gene expression levels. Furthermore, the treatments with IFN-α2a and arsenic trioxide led to the preferential suppression of the cell proliferation rate of the K562 expressing mutant JAK2 cells compared with the wild type cells, and this suppression occurred in a dose-dependent manner(p < 0.01). Moreover, the modified cells were able to differentiate into megakaryocyte-like cells following stimulation with phorbol 12 myristate 13 acetate (PMA). Taken together, the results of the present study have shown that the CRISPR/Cas9-modified JAK2 V617F model may be used as a disease model in the search of novel therapies for MPNs. Full article

(This article belongs to the Section Molecular Pharmacology)

22 pages, 1995 KiB

Open AccessReview

Virus-Induced Genome Editing (VIGE): One Step Away from an Agricultural Revolution

by Elena Mikhaylova

Int. J. Mol. Sci. 2025, 26(10), 4599; https://doi.org/10.3390/ijms26104599 (registering DOI) - 11 May 2025

Abstract

There is currently a worldwide trend towards deregulating the use of genome-edited plants. Virus-induced genome editing (VIGE) is a novel technique that utilizes viral vectors to transiently deliver clustered regularly interspaced short palindromic repeat (CRISPR) components into plant cells. It potentially allows us [...] Read more.

There is currently a worldwide trend towards deregulating the use of genome-edited plants. Virus-induced genome editing (VIGE) is a novel technique that utilizes viral vectors to transiently deliver clustered regularly interspaced short palindromic repeat (CRISPR) components into plant cells. It potentially allows us to obtain transgene-free events in any plant species in a single generation without in vitro tissue culture. This technology has great potential for agriculture and is already being applied to more than 14 plant species using more than 20 viruses. The main limitations of VIGE include insufficient vector capacity, unstable expression of CRISPR-associated (Cas) protein, plant immune reaction, host specificity, and reduced viral activity in meristem. Various solutions to these problems have been proposed, such as fusion of mobile elements, RNAi suppressors, novel miniature Cas proteins, and seed-borne viruses, but the final goal has not yet been achieved. In this review, the mechanism underlying the ability of different classes of plant viruses to transiently edit genomes is explained. It not only focuses on the latest achievements in virus-induced editing of crops but also provides suggestions for improving the technology. This review may serve as a source of new ideas for those planning to develop new approaches in VIGE. Full article

(This article belongs to the Special Issue CRISPR-Cas Systems and Genome Editing—2nd Edition)

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18 pages, 2080 KiB

Open AccessArticle

Evaluation of Low-Coverage Sequencing Strategies for Whole-Genome Imputation in Pacific Abalone Haliotis discus hannai

by Chengxia Fei, Shoudu Zhang, Xiangrui Chen, Junyu Liu, Wenzhu Peng, Guofan Zhang, Weiwei You and Fucun Wu

Int. J. Mol. Sci. 2025, 26(10), 4598; https://doi.org/10.3390/ijms26104598 (registering DOI) - 11 May 2025

Abstract

Low-coverage whole-genome sequencing (lcWGS) followed by imputation is emerging as a cost-effective method for generating a substantial number of single nucleotide polymorphism (SNP) in aquatic species with highly heterozygous and complex genomes. This study represents the first systematic investigation into the application of [...] Read more.

Low-coverage whole-genome sequencing (lcWGS) followed by imputation is emerging as a cost-effective method for generating a substantial number of single nucleotide polymorphism (SNP) in aquatic species with highly heterozygous and complex genomes. This study represents the first systematic investigation into the application of low-coverage whole-genome sequencing (lcWGS) combined with imputation for genotyping in Pacific abalone (Haliotis discus hannai) without a reference panel. We utilized 1059 Pacific abalone individuals sequenced at an average depth of 7.86×, as well as 16 individuals sequenced at 20×, as sample materials. To assess the genotype imputation accuracy for lcWGS without a reference panel, we simulated data with varying sequencing depths (0.5–4×) and examined the effects of sample size, chromosome length, and minor allele frequency (MAF) using BaseVar and STITCH strategies. Results showed that STITCH achieved high accuracy when the sample size exceeded 400, with a genotype correlation (R²) of 0.98 ± 0.002 and genotype concordance (GC) of 0.99 ± 0.001. Imputation accuracy plateaued when the sample size exceeded 400 and sequencing depth surpassed 1×. Chromosome length had minimal effects, with all three chromosomes achieving an accuracy of approximately 0.98. However, the accuracy for rare MAF (<0.05) was lower, falling below 0.99. A second imputation with Beagle significantly increased SNP detection by 3.9–8.3 folds for a sequencing depth of 0.5–4×, apparently without sacrificing accuracy. To our knowledge, this is the first study of lcWGS analysis conducted in abalone. The findings demonstrate that lcWGS with imputation can achieve high accuracy with moderate sample sizes (n ≥ 400) in Pacific abalone, offering a cost-effective approach for genotyping in aquaculture species. Full article

(This article belongs to the Special Issue Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges)

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15 pages, 5408 KiB

Open AccessArticle

An Ionic Liquid-Assisted Mixed Micelle-Mediated Centrifuge-Less Cloud Point Extraction Spectrophotometric Method for the Determination of Molybdenum(VI)

by Vidka Divarova, Andrea Gajdošová, Petya Racheva and Kiril Gavazov

Int. J. Mol. Sci. 2025, 26(10), 4597; https://doi.org/10.3390/ijms26104597 (registering DOI) - 11 May 2025

Abstract

A novel method for the spectrophotometric determination of trace amounts of molybdenum has been developed. This method utilizes a centrifuge-less cloud point extraction (CL-CPE) in a mixed micellar (MM) system containing a nonionic surfactant (Triton X-114) and an ionic liquid (Aliquat^® 336, [...] Read more.

A novel method for the spectrophotometric determination of trace amounts of molybdenum has been developed. This method utilizes a centrifuge-less cloud point extraction (CL-CPE) in a mixed micellar (MM) system containing a nonionic surfactant (Triton X-114) and an ionic liquid (Aliquat^® 336, A336). The chromophore chelating reagent employed was 4-nitrocatechol (4NC, H₂L). This work marks its first application as a CPE reagent. Under the optimal conditions, Mo(VI) forms a yellow ternary complex with 4NC and A336, which can be represented by the formula (A336⁺)₂[MoO₂L₂]. The method possesses the following characteristics: limit of detection (LOD) of 3.2 ng mL⁻¹, linear range of 10.8–580 ng/mL, absorption maximum of 435 nm, molar absorptivity coefficient of 3.34 × 10⁵ L mol⁻¹ cm⁻¹, and Sandell’s sensitivity of 0.29 ng cm⁻². The method has been successfully employed for the determination of molybdenum in reference standard steel samples, bottled mineral water, and a molybdenum-containing dietary supplement. Full article

(This article belongs to the Special Issue Molecular Applications of Technologies and Techniques for the Extraction of Simple Molecules and Compounds)

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17 pages, 3855 KiB

Open AccessArticle

Reduced Sulfur Diet Reshapes the Microbiome and Metabolome in Mild–Moderate Ulcerative Colitis

by Jiayu Ye, Maitreyi Raman, Lorian M. Taylor, Munazza Yousuf, Remo Panaccione, Christian Turbide, Sidhartha R. Sinha and Natasha Haskey

Int. J. Mol. Sci. 2025, 26(10), 4596; https://doi.org/10.3390/ijms26104596 (registering DOI) - 11 May 2025

Abstract

This pilot study investigated the effects of a reduced sulfur (RS) diet on the gut microbiome composition and fecal metabolome in individuals with remitted or active ulcerative colitis (UC). Thirteen participants maintained their habitual diet (control), while nine followed an RS diet for [...] Read more.

This pilot study investigated the effects of a reduced sulfur (RS) diet on the gut microbiome composition and fecal metabolome in individuals with remitted or active ulcerative colitis (UC). Thirteen participants maintained their habitual diet (control), while nine followed an RS diet for eight weeks (Wk8). Stool and plasma samples were collected at the baseline and Wk8. The sulfur intake decreased in the RS group (−28 g/1000 kcal) versus the control group (−1.7 g/1000 kcal; p < 0.001). The RS group exhibited a significant decrease in lipopolysaccharide-binding protein (−5280 ng/mL), while these levels increased in the control group (620 ng/mL; p < 0.05). The microbiome analysis showed an increased alpha diversity at Wk8 (p < 0.01), suggesting a microbial shift with a RS intake. The metabolic alterations indicated enhanced nitrogen disposal (increased uric acid, methyluric acid, N-acetyl-L-glutamate) and a higher energy demand (elevated ubiquinol and glucose-pyruvate). The RS diet increased beneficial microbes Collinsella stercoris, Asaccharobacter celatus, and Alistipes finegoldii, while decreasing pathobionts Eggerthella lenta and Romboutsia ilealis. Methyluric acid correlated positively with C. stercoris (β = 0.70) and negatively with E. lenta (β = −0.77) suggesting these microbes utilized this metabolite and influenced the microbiome composition. In conclusion, a RS diet promoted microbial diversity, metabolic adaptations, and reduced inflammation, highlighting its potential as a novel strategy for UC management. Full article

(This article belongs to the Special Issue Inflammatory Bowel Disease and Microbiome)

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14 pages, 4102 KiB

Open AccessArticle

Effects of Combination Treatment with Leptin and Liraglutide on Glucose Metabolism in Insulin-Dependent Diabetic Mice

by Linlin Fu, Mariko Sugiyama, Shahriar Kamal, Tsubasa Ide, Tadashi Takeda, Mitsuhiro Kuno, Hiroshi Takagi, Teruhiko Koike, Hiroshi Arima and Ryoichi Banno

Int. J. Mol. Sci. 2025, 26(10), 4595; https://doi.org/10.3390/ijms26104595 (registering DOI) - 11 May 2025

Abstract

We investigated whether the peripheral co-administration of leptin and liraglutide (a glucagon-like peptide-1 receptor agonist) improved glucose metabolism in a mouse model of insulin-dependent diabetes mellitus (IDDM). Twelve-week-old male C57BL/6J mice were injected intraperitoneally with a high dose of streptozotocin to induce IDDM [...] Read more.

We investigated whether the peripheral co-administration of leptin and liraglutide (a glucagon-like peptide-1 receptor agonist) improved glucose metabolism in a mouse model of insulin-dependent diabetes mellitus (IDDM). Twelve-week-old male C57BL/6J mice were injected intraperitoneally with a high dose of streptozotocin to induce IDDM or vehicle-treated. Mice with IDDM were divided into four groups: leptin treatment alone (LEP), liraglutide treatment alone (LIRA), co-administration of leptin and liraglutide treatment (LEP+LIRA), untreated mice (UNT). Vehicle-treated mice were the healthy controls (HC). The blood glucose (BG) levels were measured, and a glucose tolerance test (GTT) was performed to compare the five groups. Leptin was administered peripherally at 20 μg/day using an osmotic pump, while liraglutide was administered subcutaneously at 1000 μg/kg/day. Monotherapy with leptin or liraglutide significantly improved glucose metabolism, as assessed by comparing BG levels and GTTs with those of the UNT group. Mice in the LEP+LIRA group showed even greater improvements in glucose metabolism than the monotherapy groups. Notably, glucose metabolism in the LEP+LIRA group improved comparably with the HC group. Thus, the peripheral co-administration of leptin and liraglutide effectively improved glucose metabolism in mice with IDDM without the use of insulin. Full article

(This article belongs to the Special Issue The Relationship, Mechanisms, and Treatment Strategies of Diabetes Mellitus and Related Diseases)

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18 pages, 7300 KiB

Open AccessReview

Positivity Rate of PD-L1 Expression and Its Clinical Significance in Vulvar Cancer: A Systematic Review and Meta-Analysis

by Stefanos Flindris, Crysoula Margioula-Siarkou, Christos V. Chalitsios, Georgia Margioula-Siarkou, Emmanouela-Aliki Almperi, Aristarchos Almperis, Effrosyni Styliara, Konstantinos Flindris, Minas Paschopoulos, Iordanis Navrozoglou, Konstantinos K. Tsilidis, Konstantinos Dinas, Stamatios Petousis and Georgios Markozannes

Int. J. Mol. Sci. 2025, 26(10), 4594; https://doi.org/10.3390/ijms26104594 (registering DOI) - 11 May 2025

Abstract

The prevalence and prognostic value of programmed death ligand 1 (PD-L1) expression, as a potential biomarker in vulvar squamous cell carcinomas (VSCCs), remain underexplored. We searched the PubMed, Scopus, Embase, and Cochrane Library databases until July 2024 for articles examining PD-L1 expression in [...] Read more.

The prevalence and prognostic value of programmed death ligand 1 (PD-L1) expression, as a potential biomarker in vulvar squamous cell carcinomas (VSCCs), remain underexplored. We searched the PubMed, Scopus, Embase, and Cochrane Library databases until July 2024 for articles examining PD-L1 expression in VSCCs. Random-effects meta-analyses summarized PD-L1 expression overall and in subgroups by immunohistochemistry antibody type, positivity cutoff, tumor stage, and HPV positivity. Additionally, random-effects meta-analyses summarized the association between PD-L1 positivity and cancer prognosis. We included 26 studies comprising 1912 VSCC cases. The summary PD-L1 positivity rate in tumor cells was 59.9% (95% confidence interval [CI]: 47.7–71.4%; I² = 96%, n = 26), influenced by the different cutoff thresholds utilized to define PD-L1 positivity. Compared to tumor cells, positivity rates were higher in intratumoral immune cells (75.6%; 95%CI: 52.9–92.5; I² = 95.4%, n = 6) and peritumoral cells (78.9%; 95%CI: 54.4–95.5%; I² = 91%, n = 3) but with overlapping 95%CIs. No heterogeneity was observed in the rates by tumor stage or HPV status. Positive PD-L1 expression was associated with worse overall (hazard ratio [HR] = 1.43; 95%CI: 1.06–1.93; I² = 28.9%, n = 7) and progression-free survival (HR = 1.57; 95%CI: 1.07–2.3; I² = 38.3%, n = 5). The PD-L1 expression rate in VSCC tumor cells varied across studies, was influenced by differences in immunohistochemical evaluation, and was identified as an unfavorable prognostic factor. Large, prospective, multicenter studies with standardized protocols are crucial to further elucidate the clinical significance of PD-L1 expression in VSCCs. Full article

(This article belongs to the Special Issue Gynecologic Oncology: Molecular Mechanisms and Therapies)

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18 pages, 1185 KiB

Open AccessReview

Type 1 Diabetes Mellitus and Vitamin D

by Teodoro Durá-Travé and Fidel Gallinas-Victoriano

Int. J. Mol. Sci. 2025, 26(10), 4593; https://doi.org/10.3390/ijms26104593 (registering DOI) - 11 May 2025

Abstract

Type 1 diabetes mellitus (T1DM) is a multifactorial disease in which environmental factors and genetic predisposition interact to induce an autoimmune response against pancreatic β-cells. Vitamin D promotes immune tolerance through immunomodulatory and anti-inflammatory functions. The aim of this study is to provide [...] Read more.

Type 1 diabetes mellitus (T1DM) is a multifactorial disease in which environmental factors and genetic predisposition interact to induce an autoimmune response against pancreatic β-cells. Vitamin D promotes immune tolerance through immunomodulatory and anti-inflammatory functions. The aim of this study is to provide a narrative review about the association between vitamin D status in the pathogenesis of T1DM and the role of vitamin D supplementation in the prevention and treatment of T1DM. Although vitamin D deficiency is more prevalent in children/adolescents with new-onset T1DM than in healthy individuals, there does not appear to be an association between vitamin D status before diagnosis and the onset of T1DMD later in life. The results of vitamin D as adjuvant therapy have, at best, a positive short-term effect in newly diagnosed T1DM patients. Intervention studies have been conducted in the clinical phase of T1DM, but it would be desirable to do so in the early stages of the autoimmune process (pre-diabetes). Full article

(This article belongs to the Special Issue The Role of Vitamin D in Human Health and Diseases 4.0)

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17 pages, 691 KiB

Open AccessReview

Amyloid β-Induced Inflammarafts in Alzheimer’s Disease

by Shihui Ding, Soo-Ho Choi and Yury I. Miller

Int. J. Mol. Sci. 2025, 26(10), 4592; https://doi.org/10.3390/ijms26104592 (registering DOI) - 10 May 2025

Abstract

The formation of amyloid beta (Aβ) plaques is a central process in the development of Alzheimer’s disease (AD). Although its causative role or the effectiveness of therapeutic targeting is still debated, the key involvement of Aβ in the pathogenesis of neuroinflammation and neurodegeneration [...] Read more.

The formation of amyloid beta (Aβ) plaques is a central process in the development of Alzheimer’s disease (AD). Although its causative role or the effectiveness of therapeutic targeting is still debated, the key involvement of Aβ in the pathogenesis of neuroinflammation and neurodegeneration in AD is broadly accepted. In this review, we emphasize the role of lipid rafts, both in APP cleavage producing Aβ in neurons and in mediating Aβ inflammatory signaling in microglia. We introduce the term inflammarafts to characterize the Aβ-driven formation of enlarged, cholesterol-rich lipid rafts in activated microglia, which support protein–protein and lipid–protein interactions of inflammatory receptors. Examples reviewed include toll-like receptors (TLR2, TLR4), scavenger receptors (CD36, RAGE), and TREM2. The downstream pathways lead to the production of cytokines and reactive oxygen species, intensifying neuroinflammation and resulting in neuronal injury and cognitive decline. We further summarize emerging therapeutic strategies and emphasize the utility of apolipoprotein A-I binding protein (AIBP) in selective targeting of inflammarafts and attenuation of microglia-driven inflammation. Unlike the targeting of a single inflammatory receptor or a secretase, selective disruption of inflammarafts and preservation of physiological lipid rafts offer a novel approach to targeting multiple components and processes that contribute to neuroinflammation in AD. Full article

(This article belongs to the Special Issue Advances in the Search for Protective Agents against Amyloid β-Induced Brain Degeneration)

26 pages, 5996 KiB

Open AccessArticle

N-N-Substituted Piperazine, Cmp2, Improves Cognitive and Motor Functions in 5xFAD Mice

by Nikita Zernov, Daria Melenteva, Viktor Ghamaryan, Ani Makichyan, Lernik Hunanyan and Elena Popugaeva

Int. J. Mol. Sci. 2025, 26(10), 4591; https://doi.org/10.3390/ijms26104591 (registering DOI) - 10 May 2025

Abstract

The piperazine derivative N-(2,6-difluorophenyl)-2-(4-phenylpiperazin-1-yl)propanamide (cmp2) has emerged as a potential transient receptor potential cation channel, subfamily C, member 6 (TRPC6) modulator, offering a promising pathway for Alzheimer’s disease (AD) therapy. Our recent findings identify cmp2 as a novel compound with synaptoprotective effects in [...] Read more.

The piperazine derivative N-(2,6-difluorophenyl)-2-(4-phenylpiperazin-1-yl)propanamide (cmp2) has emerged as a potential transient receptor potential cation channel, subfamily C, member 6 (TRPC6) modulator, offering a promising pathway for Alzheimer’s disease (AD) therapy. Our recent findings identify cmp2 as a novel compound with synaptoprotective effects in primary hippocampal cultures and effective blood–brain barrier (BBB) penetration. In vivo studies demonstrate that cmp2 (10 mg/kg, intraperitoneally) restores synaptic plasticity deficits in 5xFAD mice. This study further shows cmp2’s selectivity towards tetrameric TRPC6 channel in silico. Acute administration of cmp2 is non-toxic, with no indications of chronic toxicity, and Ames testing confirms its lack of mutagenicity. Behavioral assays reveal that cmp2 improves cognitive functions in 5xFAD mice, including increased novel object recognition, better passing of the Morris water maze, and improved fear memory, as well as upregulation of motor function in beam walking tests. These findings suggest that cmp2 holds promise as a candidate for AD treatment. Full article

(This article belongs to the Special Issue Drug Design and Development for Neurological Diseases)

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12 pages, 2801 KiB

Open AccessArticle

A High-Throughput Cell-Based Luciferase Reporter Assay for Identifying Inhibitors of ASGR1

by Lingmin Gan, Haoyu Zou, Zhaoqi Yang, Juntao Wang, Yunzhi Sheng, Pengfei Du, Shikun Zhang and Zili Feng

Int. J. Mol. Sci. 2025, 26(10), 4590; https://doi.org/10.3390/ijms26104590 (registering DOI) - 10 May 2025

Abstract

The asialoglycoprotein receptor 1 (ASGR1) represents a highly promising target for drug development, with its expression regulation closely linked to various diseases. Consequently, research concentrating on targeted therapies against ASGR1 holds significant importance in devising effective treatment strategies. In this study, we utilized [...] Read more.

The asialoglycoprotein receptor 1 (ASGR1) represents a highly promising target for drug development, with its expression regulation closely linked to various diseases. Consequently, research concentrating on targeted therapies against ASGR1 holds significant importance in devising effective treatment strategies. In this study, we utilized the CRISPR-Knockin technology to insert a firely luciferase reporter gene downstream of exon 9 of the ASGR1 gene in HepG2 cell line. This modification enables the expression level of luciferase to be directly proportional to the activity intensity of the ASGR1 protein. We successfully established a drug screening and evaluation model for ASGR1 and employed it for high-throughput screening of potential inhibitors from a microbial molecular metabolite library. After our screening process, several promising candidates were identified as potential ASGR1 inhibitors. Western blotting experiment was conducted to validate the efficacy of our drug screening model, thereby providing a solid experimental foundation for the development of novel targeted therapeutics targeting ASGR1. Full article

(This article belongs to the Special Issue Targeting of Functional Proteins in Disease Therapeutics: Enzyme Function and Inhibition Studies)

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31 pages, 3989 KiB

Open AccessArticle

Early Zinc Supplementation Enhances Epididymal Sperm Glycosylation, Endocrine Activity, and Antioxidant Activity in Rats Exposed to Cadmium

by Sergio Marín de Jesús, Rosa María Vigueras-Villaseñor, Edith Cortés-Barberena, Joel Hernández-Rodríguez, Sonia Guadalupe Pérez-Aguirre, Sergio Montes, Leticia Carrizales-Yáñez, Isabel Arrieta-Cruz and Marcela Arteaga-Silva

Int. J. Mol. Sci. 2025, 26(10), 4589; https://doi.org/10.3390/ijms26104589 (registering DOI) - 10 May 2025

Abstract

Sperm maturation involves changes in plasma membrane glycosylation for fertilization. Cadmium (Cd) exerts a negative effect by disrupting testicular and epididymal function, altering antioxidant activity. Zinc (Zn) is an essential element known for its antioxidant properties, role in testosterone synthesis, and support of [...] Read more.

Sperm maturation involves changes in plasma membrane glycosylation for fertilization. Cadmium (Cd) exerts a negative effect by disrupting testicular and epididymal function, altering antioxidant activity. Zinc (Zn) is an essential element known for its antioxidant properties, role in testosterone synthesis, and support of spermatogenesis. However, its effect on sperm membrane glycosylation, as well as endocrine and antioxidant activity, after exposure to Cd has remained unexplored. This study evaluated the impact of Zn on epididymal sperm glycosylation, endocrine activity, and antioxidant activity in Cd-exposed rats. Four groups of male Wistar rats were analyzed: control, Cd-exposed, Zn-supplemented, and Zn + Cd groups. On postnatal day 90, tissues and blood were collected for Zn and Cd quantification, testosterone levels, antioxidant activity, histological analysis, and sperm quality. The results showed that Cd concentration increased significantly, reduced testosterone levels, modified antioxidant activity, and caused structural damage in the epididymis. The Cd-exposed group showed disrupted glycosylation and distribution patterns and reduced sperm quality. The Zn + Cd group showed lower Cd accumulation, preserved testosterone levels, restored antioxidant activity, and preserved glycosylation patterns and sperm quality. This study highlights the protective role of Zn in mitigating Cd-induced reproductive toxicity, probably through the competitive inhibition of Cd uptake and antioxidant support, thereby preserving fertility. Full article

(This article belongs to the Special Issue Advances in Spermatogenesis and Male Infertility)

16 pages, 2733 KiB

Open AccessArticle

Ergosterol Peroxide Disrupts Triple-Negative Breast Cancer Mitochondrial Function and Inhibits Tumor Growth and Metastasis

by Aliyah L. Bocachica-Adorno, Adriana Y. Aponte-Ramos, Paola S. Rivera-Fuentes, Natalia P. Espinosa-Ponce, Luz V. Arroyo-Cruz, Taotao Ling, Naydi Pérez-Ríos, Sona Rivas-Tumanyan, Israel A. Almodóvar-Rivera, Carlos Barreto-Gamarra, Maribella Domenech-García, Fatima Rivas and Michelle M. Martínez-Montemayor

Int. J. Mol. Sci. 2025, 26(10), 4588; https://doi.org/10.3390/ijms26104588 (registering DOI) - 10 May 2025

Abstract

Ergosterol peroxide (EP) triggers apoptosis pathways by inducing reactive oxygen species (ROS) in TNBC cell lines. Excess ROS production is associated with major damage to mitochondria. We hypothesized that EP may act through ROS-induced mitochondrial dysfunction. Therefore, we performed a series of assays [...] Read more.

Ergosterol peroxide (EP) triggers apoptosis pathways by inducing reactive oxygen species (ROS) in TNBC cell lines. Excess ROS production is associated with major damage to mitochondria. We hypothesized that EP may act through ROS-induced mitochondrial dysfunction. Therefore, we performed a series of assays that assessed mitochondrial membrane potential (MMP), cellular respiration, and glycolysis in TNBC models. Cardiomyocytes derived from human-induced pluripotent stem cells were chosen as a non-cancerous model because of their high mitochondrial content. Two in vivo TNBC models were used to quantify the effect of EP on tumor volume and metastases. EP reduced MMP and disrupted mitochondrial functions exclusively in TNBC cells. In vivo EP was effective in reducing tumor volume without affecting liver function. There was also a significant decrease in metastasis to the lung, liver, and cancer stem cells following treatment. These results suggest EP is a promising therapy for TNBC. Full article

(This article belongs to the Special Issue Breast Cancer: From Pathophysiology to Novel Therapies)

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