International Journal of Molecular Sciences

23 pages, 10573 KB

Open AccessArticle

Exposure to Bisphenol B and S Increases the Risk of Male Reproductive Dysfunction in Middle Age

by Sen Zhao, Heliang Ni, Yuan Xiao, Jing Du, Yudong Han, Wenying Wang, Shuang Tang and Mingxi Yu

Int. J. Mol. Sci. 2025, 26(19), 9507; https://doi.org/10.3390/ijms26199507 (registering DOI) - 28 Sep 2025

Abstract

Accumulating evidence indicates that bisphenol A (BPA) analogs, including bisphenol B (BPB) and bisphenol S (BPS), disrupt testicular function and contribute to male reproductive dysfunction (MRD). However, whether BPA analogs are involved in MRD among middle-aged men remains inconclusive. Therefore, we selected cryptorchidism, [...] Read more.

Accumulating evidence indicates that bisphenol A (BPA) analogs, including bisphenol B (BPB) and bisphenol S (BPS), disrupt testicular function and contribute to male reproductive dysfunction (MRD). However, whether BPA analogs are involved in MRD among middle-aged men remains inconclusive. Therefore, we selected cryptorchidism, erectile dysfunction, premature ejaculation, and testicular tumors as representative MRD conditions in middle-aged individuals, aiming to explore the molecular mechanisms that may be disrupted by bisphenols (BPs). By using GeneCards, STRING and Cytoscape, TP53, AKT1, and MYC were pinpointed as core targets associated with MRD. Enrichment analysis suggested that BPs may induce MRD by disrupting steroidogenesis. UPLC-MS/MS analysis showed that both BPB and BPS exhibit specific accumulation in the testes. Following 20-day exposure to 0.3 or 0.6 mg/kg body weight/day BPB or BPS, testosterone levels and the expression of hub genes were decreased. The molecular docking results demonstrated that both BPB and BPS can directly bind to members of the cytochrome P450 family, potentially interfering with sex hormone biosynthesis. Our study identified the targets and mechanisms through which BPB and BPS induce MRD in middle-aged males, thereby providing insights for the safety assessment of BPs. Full article

(This article belongs to the Special Issue Molecular Biology of Human Reproduction)

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15 pages, 634 KB

Open AccessArticle

The Human Alpha3 Beta2 Neuronal Nicotinic Acetylcholine Receptor Can Form Two Distinguishable Subtypes

by Doris C. Jackson, Marcel K. Hall and Sterling N. Sudweeks

Int. J. Mol. Sci. 2025, 26(19), 9506; https://doi.org/10.3390/ijms26199506 (registering DOI) - 28 Sep 2025

Abstract

Diverse neuronal nicotinic acetylcholine receptor (nAChR) subtypes are expressed in hippocampal interneurons. Single-cell analysis of mRNA expression previously revealed prominent co-expression of the α3 and β2 subunits within rat interneurons in the CA1 region. Although the α3 subunit (traditionally expressed together with β4) [...] Read more.

Diverse neuronal nicotinic acetylcholine receptor (nAChR) subtypes are expressed in hippocampal interneurons. Single-cell analysis of mRNA expression previously revealed prominent co-expression of the α3 and β2 subunits within rat interneurons in the CA1 region. Although the α3 subunit (traditionally expressed together with β4) is usually associated with the peripheral nervous system, its significant co-expression with the β2 subunit in hippocampal interneurons suggests a distinct, potentially novel central nervous system nAChR subtype. We demonstrate that the human α3 and β2 subunits injected into Xenopus laevis oocytes can assemble into at least two functionally distinct subtypes of nAChRs based on different subunit stoichiometries. These subtypes exhibit similar reversal potentials but differ significantly in their desensitization kinetics and acetylcholine (ACh) affinities. The response obtained from a 1:5 α3:β2 mRNA injection ratio shows a higher affinity for ACh and significantly greater desensitization during prolonged ACh application compared to the response obtained from a 5:1 α3:β2 mRNA injection ratio. The identification of distinct functional α3β2 subtypes, characterized by differential desensitization kinetics and ACh affinity, could represent novel targets for the potential development of highly selective cognitive therapeutics for conditions such as Alzheimer’s disease, autism spectrum disorder, and attention deficit hyperactivity disorder, where hippocampal nAChRs are implicated. Full article

(This article belongs to the Special Issue New Research Progresses on Multifaceted Cholinergic Signaling)

20 pages, 4766 KB

Open AccessArticle

Gibberellin Disrupts Hormonal Homeostasis and Anther Integrity to Trigger Sex Reversal in Spinach

by Tengqi Wang, Ehsan Khalid, Haoming Mao, Yihan Tong, Xinyu Xue, Yuru Tang, Lingmin Cai and Ray Ming

Int. J. Mol. Sci. 2025, 26(19), 9505; https://doi.org/10.3390/ijms26199505 (registering DOI) - 28 Sep 2025

Abstract

Spinach is a dioecious vegetable and an excellent model for investigating plant sex differentiation. Exogenous gibberellin treatment induced sepal hypoplasia and sex reversal, converting 42% of stamens into pistils in male plants. Transcriptome analysis identified 112 male-biased genes enriched in stamen and pollen [...] Read more.

Spinach is a dioecious vegetable and an excellent model for investigating plant sex differentiation. Exogenous gibberellin treatment induced sepal hypoplasia and sex reversal, converting 42% of stamens into pistils in male plants. Transcriptome analysis identified 112 male-biased genes enriched in stamen and pollen development, while hormone profiling revealed coordinated changes in GA, cytokinins, auxin, jasmonic acid, and abscisic acid. Functional assays demonstrated that silencing SpAMS or SpPGIP caused extensive carpelization, and in situ hybridization localized their expression to developing anthers. Dual-luciferase assays confirmed that SpAMS directly activates the B-class gene SpPI, and genomic mapping placed SpAMS in the pseudo-autosomal region of the Y chromosome. These results indicate that GA disrupts hormonal homeostasis and anther wall integrity, while the SpAMS–SpPI pathway regulates tapetal development to maintain male identity. Our findings identify SpAMS as a key male-promoting factor in spinach and provide a framework for elucidating sex determination mechanisms in dioecious plants. Full article

(This article belongs to the Section Molecular Plant Sciences)

21 pages, 1826 KB

Open AccessArticle

Study of the Patterns of DNA Methylation in Human Cells Through the Prism of Intra-Strand DNA Symmetry

by Zamart Ramazanova, Aizhan Alikul, Dinara Begimbetova, Sabira Taipakova, Bakhyt T. Matkarimov and Murat Saparbaev

Int. J. Mol. Sci. 2025, 26(19), 9504; https://doi.org/10.3390/ijms26199504 (registering DOI) - 28 Sep 2025

Abstract

Cellular organisms store heritable information in two forms, genetic and epigenetic, the latter being largely dependent on cytosine methylation (5mC). Chargaff’s Second Parity Rule (CSPR) describes the nucleotide composition of cellular genomes in terms of intra-strand DNA symmetry. However, it remains unknown whether [...] Read more.

Cellular organisms store heritable information in two forms, genetic and epigenetic, the latter being largely dependent on cytosine methylation (5mC). Chargaff’s Second Parity Rule (CSPR) describes the nucleotide composition of cellular genomes in terms of intra-strand DNA symmetry. However, it remains unknown whether DNA methylation patterns display intra-strand DNA symmetry. Computational analysis was conducted of the DNA methylation patterns observed in human cell lines and in tissue samples from healthy donors. Analysis of 5mC marks in mutually reverse-complementary pairs of short oligomers, containing CpG dinucleotide in the middle, revealed deviations from CSPR and methylation asymmetry that can be observed for two non-overlapping mirror groups defined by CpG methylation values. Deviations from CSPR, together with combinatorial probabilities of pattern distributions and computer simulations, highlight the non-random nature of methylation processes and enabled us to identify specific cell types as outliers. Further analysis revealed a compensatory methylation asymmetry that reduces deviations from intra-strand symmetry and implies the existence of strand-specific methylation during cell differentiation. Among six pairs of reverse-complementary tetranucleotides, four pairs with specific sequence motifs display pronounced methylation asymmetry. This mirror asymmetry may be associated with chromosome folding and the formation of a complex three-dimensional landscape. Full article

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

19 pages, 2491 KB

Open AccessCommunication

Osteoporosis-Improving Effects of Extracellular Vesicles from Human Amniotic Membrane Stem Cells in Ovariectomized Rats

by Ka Young Kim, Khan-Erdene Tsolmon, Zolzaya Bavuu, Chan Ho Noh, Hyun-Soo Kim, Heon-Sang Jeong, Dongsun Park, Soon-Cheol Hong and Yun-Bae Kim

Int. J. Mol. Sci. 2025, 26(19), 9503; https://doi.org/10.3390/ijms26199503 (registering DOI) - 28 Sep 2025

Abstract

Osteoporosis is a common skeletal disease characterized by decreased bone density, leading to bone fragility and fractures, especially in menopausal women. The purpose of this study is to confirm the anti-osteoporosis activity of stem cell extracellular vesicles (EVs) as a material of regenerative [...] Read more.

Osteoporosis is a common skeletal disease characterized by decreased bone density, leading to bone fragility and fractures, especially in menopausal women. The purpose of this study is to confirm the anti-osteoporosis activity of stem cell extracellular vesicles (EVs) as a material of regenerative medicine. Mesenchymal stem cells have a potential to differentiate into osteocytes, so directly reconstruct bone tissue or facilitate bone regeneration via paracrine effects. Paracrine effects are mediated by functional molecules delivered in EVs released from stem cells. EVs containing high concentrations of growth factors (GFs) and neurotrophic factors (NFs) were attained via hypoxia culture of human amniotic membrane stem cells (AMSCs). From the EVs with a mean diameter of 77 nm, 751 proteins and 15 species of lipids were identified. Sprague-Dawley rats were ovariectomized, and eight weeks later, intravenously injected with EVs at doses of 1 × 10⁸, 3 × 10⁸ or 1 × 10⁹ particles/100 μL/body, weekly for eight weeks. One week after the final administration, the serum and bone parameters related to bone density were analyzed. Serum 17β-estradiol, alkaline phosphatase, and calcium levels that decreased in ovariectomized rats were restored by EVs in a dose-dependent manner. Bone parameters such as bone mineral density, bone mineral content, bone volume/tissue volume ratio, trabecular number, trabecular space, and bending strength were also improved by treatment with EVs. Such effects were confirmed by morphological findings of micro-computed tomography. Taken together, it is suggested that AMSC-EVs containing high concentrations of GFs and NFs preserve bone soundness by promoting bone regeneration and inhibiting bone resorption. Full article

(This article belongs to the Special Issue Stem Cells in Health and Disease: 3rd Edition)

25 pages, 2079 KB

Open AccessReview

Dynamic Hydrogels: Adaptive Biomaterials for Engineering Tumor Microenvironment and Cancer Treatment

by Yuting Wu, Yifei Xiao, Bohan Yin and Siu Hong Dexter Wong

Int. J. Mol. Sci. 2025, 26(19), 9502; https://doi.org/10.3390/ijms26199502 (registering DOI) - 28 Sep 2025

Abstract

Dynamic hydrogels are revolutionizing tumor microenvironment (TME) engineering through their stimuli-responsive adaptability, mechanical tunability, and capacity for multifunctional integration. In addition, they are excellent biomaterials for cancer treatments, including their biomimetic properties and controlled cargo release capability. This review introduces the rational design [...] Read more.

Dynamic hydrogels are revolutionizing tumor microenvironment (TME) engineering through their stimuli-responsive adaptability, mechanical tunability, and capacity for multifunctional integration. In addition, they are excellent biomaterials for cancer treatments, including their biomimetic properties and controlled cargo release capability. This review introduces the rational design and principles of dynamic hydrogels for recreating the tumor microenvironment and cancer therapy, including natural/synthetic hydrogels, multi-stimuli responsive hydrogels, and multi-drug loading hydrogels. These designs emphasize their unique roles in overcoming drug resistance, enhancing immunotherapy, and enabling patient-specific models. We highlight breakthroughs such as dual-responsive nanocomposites and microfluidic-integrated 3D platforms while addressing translational hurdles like cytotoxicity and regulatory delays. By proposing strategies to bridge material science with clinical needs, this work positions dynamic hydrogels as pivotal tools for next-generation precision oncology. Full article

(This article belongs to the Special Issue Next-Generation Hydrogels: Innovations in Biofunctionalization and Personalization for Targeted Biomedical Therapies)

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21 pages, 2060 KB

Open AccessArticle

Development of an On-DNA Platform Molecule Bearing a Diazidestructure and Its Application to DEL Synthesis

by Hiroyuki Miyachi, Masaki Koshimizu, Manussada Ratanasak, Yasuteru Shigeta and Masashi Suzuki

Int. J. Mol. Sci. 2025, 26(19), 9501; https://doi.org/10.3390/ijms26199501 (registering DOI) - 28 Sep 2025

Abstract

Expanding the chemical space of DNA-encoded libraries (DELs) is desirable for identifying novel bioactive compounds and enhancing hit quality in affinity-based screening. In this study, we designed and synthesized a new on-DNA diazide platform (DAP) molecule that incorporates both aromatic and aliphatic azido [...] Read more.

Expanding the chemical space of DNA-encoded libraries (DELs) is desirable for identifying novel bioactive compounds and enhancing hit quality in affinity-based screening. In this study, we designed and synthesized a new on-DNA diazide platform (DAP) molecule that incorporates both aromatic and aliphatic azido groups within a single scaffold. These orthogonal azides exhibit distinct reactivity profiles, enabling a stepwise warhead construction strategy through chemoselective transformations. This approach facilitates greater structural diversity and efficient incorporation of diverse building blocks. A virtual DEL was generated based on this DAP scaffold, and its chemical space was compared with that of bioactive compounds in the ChEMBL database. The analysis revealed that this virtual library occupied a distinct and previously unexplored region of chemical space, highlighting the potential of this DAP-based strategy for discovering structurally novel DEL members with biological relevance. Full article

(This article belongs to the Section Biochemistry)

24 pages, 967 KB

Open AccessArticle

Effects of Aerobic-Resistance Training and Nutritional Intervention on Adiponectin, Interleukin-6, and hs-CRP Concentrations in Men with Abdominal Obesity—A Randomized Controlled Trial

by Karol Makiel, Aneta Targosz, Piotr Kosowski and Agnieszka Suder

Int. J. Mol. Sci. 2025, 26(19), 9500; https://doi.org/10.3390/ijms26199500 (registering DOI) - 28 Sep 2025

Abstract

The objective of this study was to assess the changes in adiponectin concentrations and inflammatory markers in men with abdominal obesity following physical exercise and exercise combined with dietary intervention. This study included 44 males with abdominal obesity (mean age 34.7 ± 5.5 [...] Read more.

The objective of this study was to assess the changes in adiponectin concentrations and inflammatory markers in men with abdominal obesity following physical exercise and exercise combined with dietary intervention. This study included 44 males with abdominal obesity (mean age 34.7 ± 5.5 years, waist circumference [WC] 110.3 ± 8.5, BMI 32.0 ± 3.9), who were randomly assigned to three groups: a control group without interventions (CG, n = 12), an experimental group engaging in aerobic-resistance exercise (EG, n = 16) and a group engaging in aerobic-resistance exercise combined with an ad libitum high-protein, low-glycemic index carbohydrate diet (EDG, n = 16). Body composition metrics: the body fat-, fat-free mass-, and abdominal fat-to body mass (BF/BM, FFM/BM, ABD/BM) indexes and the body adiposity index (BAI), along with biochemical blood analyses—adiponectin (ADIPO), interleukin-6 (IL-6), high-sensitivity C-reactive protein (hs-CRP), Castelli-II Index (CRI II) and fasting glucose–insulin (FG/I) ratio—were measured at baseline and after the intervention. The effects of the interventions on the analyzed variables across groups were assessed using mixed ANOVA tests with post hoc comparisons. Effect size (ES) was also calculated using partial eta squared (ηp²). The exercise intervention (EG) resulted in a significant reduction in the BAI (p < 0.01), insulin resistance FG/I (p < 0.02), and IL-6 concentrations (p < 0.01) and initiated an increase in ADIPO secretion (p = 0.03). The combined intervention (EDG) reduced the insulin resistance FG/I (p = 0.02) and atherogenic index CRI II (p = 0.01), decreased inflammatory markers IL-6 (p = 0.01) by 48% and hs-CRP (p = 0.04) by 30%, and simultaneously increased the ADIPO (p = 0.02) concentration by 15%. These effects were accompanied by significant changes in body composition: reductions in visceral fat ABD/BM (p < 0.01), total fat BF/BM (p < 0.01), and BAI (p = 0.02) and an increase in FFM/BM (p < 0.01). A crucial role in achieving these outcomes was played by dietary modifications, i.e., the inclusion of low-glycemic index carbohydrates (p < 0.01), a 23% increase in protein intake (p < 0.01), and a 50% increase in dietary fiber intake (p < 0.01), which consistently deepened the energy deficit (p < 0.01) and reduced fat intake (p < 0.01). These findings underscore that short-term interventions, whether exercise alone or combined with dietary modifications, can effectively reduce inflammation and lower insulin resistance in men with visceral obesity. However, the combined intervention, involving both exercise and dietary modifications, resulted in more pronounced beneficial changes in both body composition and concentrations of adipokines, inflammatory markers, and atherogenic indices and insulin resistance. Full article

(This article belongs to the Special Issue New Insights into Adipose Tissue Metabolic Function and Dysfunction, 4th Edition)

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17 pages, 1034 KB

Open AccessArticle

Serum VEGF Potential as a Biomarker for Diagnosis of Female Unexplained Infertility: Does Atopy Matter?

by Gabija Didžiokaitė, Austėja Grudytė, Aida Kuznecovaitė, Margarita Žvirblė, Žilvinas Survila, Vita Pašukonienė and Violeta Kvedarienė

Int. J. Mol. Sci. 2025, 26(19), 9499; https://doi.org/10.3390/ijms26199499 (registering DOI) - 28 Sep 2025

Abstract

Unexplained infertility (UI) remains a diagnostic challenge affecting a significant proportion of women of reproductive age. Vascular endothelial growth factor (VEGF), a key mediator of angiogenesis and inflammation, has been implicated in reproductive and immune processes. This prospective observational study evaluated serum VEGF [...] Read more.

Unexplained infertility (UI) remains a diagnostic challenge affecting a significant proportion of women of reproductive age. Vascular endothelial growth factor (VEGF), a key mediator of angiogenesis and inflammation, has been implicated in reproductive and immune processes. This prospective observational study evaluated serum VEGF levels and allergen sensitization (via ALEX² macroarray) in 70 women—51 with UI and 19 fertile controls—to assess VEGF’s potential as a biomarker in UI. Median VEGF concentrations were higher in women with UI compared to fertile controls (128.6 pg/mL vs. 82.5 pg/mL), though not statistically significantly. However, sensitized women showed significantly elevated VEGF levels compared to non-sensitized peers (115.9 pg/mL vs. 85.7 pg/mL, p = 0.028), and a stepwise increase in VEGF was observed with rising allergy severity (p = 0.045). Sensitization to pet allergens, particularly cat allergen Fel d 1, was associated with the highest VEGF levels. A literature review confirmed wide variability in VEGF concentrations and the lack of standardized norms. While VEGF alone may not serve as a definitive biomarker for infertility, elevated levels may reflect an underlying inflammatory state. Our findings suggest VEGF testing could support broader clinical evaluation in women with UI, especially in the presence of allergic sensitization. Full article

(This article belongs to the Special Issue Molecular Insights into Reproductive Biology and Related Diseases)

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76 pages, 10253 KB

Open AccessReview

Integrating Inflammatory and Epigenetic Signatures in IBD-Associated Colorectal Carcinogenesis: Models, Mechanisms, and Clinical Implications

by Kostas A. Triantaphyllopoulos, Nikolia D. Ragia, Maria-Chara E. Panagiotopoulou and Thomae G. Sourlingas

Int. J. Mol. Sci. 2025, 26(19), 9498; https://doi.org/10.3390/ijms26199498 (registering DOI) - 28 Sep 2025

Abstract

The rising global prevalence of inflammatory bowel diseases, including Crohn’s disease and ulcerative colitis, is paralleled by an increased risk of colitis-associated colorectal cancer. Persistent intestinal inflammation promotes genetic instability and epigenetic reprogramming within epithelial and immune cells, driving the multistep transition from [...] Read more.

The rising global prevalence of inflammatory bowel diseases, including Crohn’s disease and ulcerative colitis, is paralleled by an increased risk of colitis-associated colorectal cancer. Persistent intestinal inflammation promotes genetic instability and epigenetic reprogramming within epithelial and immune cells, driving the multistep transition from inflammation to neoplasia. This review integrates human and preclinical model evidence with literature mining and bioinformatic analyses of genetic, epigenetic, and ncRNA data to dissect molecular mechanisms driving colitis-associated colorectal cancer from chronic inflammation. We highlight how pro-inflammatory cytokines (e.g., TNF-α, IL-6), oxidative stress, and microbial dysbiosis converge on key transcriptional regulators such as NF-κB and STAT3, inducing DNA methylation and histone modifications (e.g., H3K27me3); altering chromatin dynamics, gene expression, and non-coding RNA networks (e.g., miR-21, MALAT1, CRNDE); ultimately reshaping pathways involved in proliferation, apoptosis, and immune evasion. This review updates new potential associations of entities with these diseases, in their networks of interaction, summarizing major aspects of genetic and chromatin-level regulatory mechanisms in inflammatory bowel disease and colorectal cancer, and emphasizing how these interactions drive the inflammatory-to-neoplastic transition. By underscoring the reversibility of epigenetic changes, we explore their translational potential in early detection, surveillance, and precision epigenetic therapy. Understanding the interplay between genetic mutations and chromatin remodeling provides a roadmap for improving diagnostics and personalized treatments in inflammatory bowel disease-associated colorectal carcinogenesis. Full article

(This article belongs to the Special Issue Molecular Research on Inflammatory Diseases of the Gut in Humans and Animals)

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22 pages, 5536 KB

Open AccessArticle

α-Glucosidase Inhibition-Guided Network Pharmacology and Molecular Docking Reveal the Antidiabetic Potential of Cichorium intybus as a Functional Food

by Abdul Bari Shah, Aizhamal Baiseitova, Ulpan Amzeyeva, Xiaofei Shang and Janar Jenis

Int. J. Mol. Sci. 2025, 26(19), 9497; https://doi.org/10.3390/ijms26199497 (registering DOI) - 28 Sep 2025

Abstract

Cichorium intybus, commonly known as chicory, is acknowledged as a substitute for coffee and is widely utilized in medicinal applications to treat various ailments. Chicory extract is commonly used in the management of diabetes; however, the specific bioactive components remain unidentified. The [...] Read more.

Cichorium intybus, commonly known as chicory, is acknowledged as a substitute for coffee and is widely utilized in medicinal applications to treat various ailments. Chicory extract is commonly used in the management of diabetes; however, the specific bioactive components remain unidentified. The present study displayed the antidiabetic potential of chicory using a comprehensive approach integrating in vitro, network pharmacology, and in silico techniques. The methanolic extract demonstrated significant α-glucosidase inhibitory activity in the initial experiment, indicating potential for the management of postprandial hyperglycemia. Based on this, chicory’s major metabolites were identified and examined for their interactions with (type 2 diabetes) T2D targets using network pharmacology. The core genes and pathways involved in the disease were mapped to understand the multitarget mechanisms of the extract. A molecular docking study validated the binding affinity and interactions of leading bioactive compounds with T2D protein targets. The findings indicate that chicory metabolites may serve as promising candidates for the development of natural antidiabetic agents. Full article

(This article belongs to the Special Issue Molecular Mechanism Discovery of the Bioactive Phytochemicals Against Different Diseases Based on Network Pharmacology and Molecular Docking, 2nd Edition)

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16 pages, 2588 KB

Open AccessArticle

Procoagulant Effects of Bothrops diporus Venom: Kinetic Modeling and Role of Serine Protease Activity

by Gisela L. Lopez, Sarah A. Nielsen, Vance G. Nielsen and Luciano S. Fusco

Int. J. Mol. Sci. 2025, 26(19), 9496; https://doi.org/10.3390/ijms26199496 (registering DOI) - 28 Sep 2025

Abstract

Bothrops species are responsible for the majority of envenomations in Argentina. In particular, Bothrops diporus is among the main species responsible for the majority of envenomations in Argentina and causes significant injury and coagulopathy. Given the significance of this venom, the authors sought [...] Read more.

Bothrops species are responsible for the majority of envenomations in Argentina. In particular, Bothrops diporus is among the main species responsible for the majority of envenomations in Argentina and causes significant injury and coagulopathy. Given the significance of this venom, the authors sought to define the toxin responsible for coagulopathy with specialized spectrophotometric and thromboelastographic methods. Utilizing clotting time, spectrophotometry, and thromboelastography, it was determined that B. diporus venom has potent, procoagulant activity in human plasma and buffer milieu. Calcium-dependent and -independent activities consistent with serine protease activity were identified. The activity included both thrombin-generating and thrombin-like enzymatic activity. The venom cleaved the serine protease-specific chromogenic substrate β-Ala-Gly-Arg-p-nitroanilide diacetate, and its activity was inhibited in plasma by antithrombin after addition of heparin. Further, venom exposed in isolation to RuCl₃, a known inhibitor of serine protease-containing venoms, demonstrated decreased activity in human plasma. In conclusion, the present study contributes to a better understanding of B. diporus venom and may have implications for the rational design of inhibitors, antivenom formulations, or preclinical models to study venom-induced coagulopathies. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Venom and Antivenom)

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18 pages, 1097 KB

Open AccessReview

Pharmacokinetic Alterations in Patients with Chronic Heart Failure: A Systematic Review

by Olga Butranova, Sergey Zyryanov and Yury Kustov

Int. J. Mol. Sci. 2025, 26(19), 9495; https://doi.org/10.3390/ijms26199495 (registering DOI) - 28 Sep 2025

Abstract

(1) Chronic heart failure (CHF) is a typical component of the polymorbid profile of an elderly patient. The aim of this systematic review was to search for data from pharmacokinetic (PK) studies of any drugs in patients with CHF to systematize information on [...] Read more.

(1) Chronic heart failure (CHF) is a typical component of the polymorbid profile of an elderly patient. The aim of this systematic review was to search for data from pharmacokinetic (PK) studies of any drugs in patients with CHF to systematize information on changes in PK parameters depending on the physicochemical properties (PCPs) of the drug and route of its administration. (2) A systematic review of PK studies in patients with CHF was performed using Elibrary.ru, United States National Library of Medicine (PubMed), China National Knowledge Infrastructure (CNKI), and Directory of Open Access Journals (DOAJ). The final number of included articles was 106. A descriptive and correlation analysis of PK data and PCPs of drugs included in the study was carried out. Inclusion criteria: PK study, available PK parameters, demographic data, and diagnosed CHF. Risk of bias was assessed using ROBINS-I. (3) Evaluation of correlations between PCPs of drugs and their PK revealed a link between (i) plasma protein binding (PPB) and volume of distribution for lipophilic drugs; (ii) PCPs, half-life, and clearance for drugs with high PPB; and (iii) PPB and clearance for hydrophilic and amphiphilic drugs. (4) Hypoalbuminemia associated with CHF may lead to an increased volume of distribution of lipophilic drugs; lipophilic drugs used in CHF patients may be associated with prolongation of the half-life period and reduction in clearance; highly protein-bound drugs may manifest with reduced clearance. PK characteristics identified in this review should guide modifications to dosing regimens in CHF patients receiving medications from different groups. Full article

(This article belongs to the Special Issue Advanced Molecular Research on Chronic Heart Failure)

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17 pages, 1552 KB

Open AccessArticle

Defective IgG Class Switching in the Spleen of TRAF5-Deficient Mice Reveals a Role for TRAF5 in CD40-Mediated B Cell Responses During Obesity-Associated Inflammation

by Tomomi Wakaizumi, Mari Hikosaka-Kuniishi, Yusuke Ozawa, Ayaka Sato, Chieri Iwata, Tsutomu Wada, Toshiyasu Sasaoka, Masashi Morita and Takanori So

Int. J. Mol. Sci. 2025, 26(19), 9494; https://doi.org/10.3390/ijms26199494 (registering DOI) - 28 Sep 2025

Abstract

Tumor necrosis factor receptor-associated factors (TRAFs) are a family of adaptor proteins that transmit signals from immunoregulatory receptors—such as TNF receptors, Toll-like receptors, and interleukin receptors—to coordinate immune and inflammatory responses. Among them, TRAF5 is highly expressed in lymphocytes and implicated in obesity-associated [...] Read more.

Tumor necrosis factor receptor-associated factors (TRAFs) are a family of adaptor proteins that transmit signals from immunoregulatory receptors—such as TNF receptors, Toll-like receptors, and interleukin receptors—to coordinate immune and inflammatory responses. Among them, TRAF5 is highly expressed in lymphocytes and implicated in obesity-associated inflammation, but its role in secondary lymphoid organs during chronic low-grade inflammation remains unclear. We examined splenic B and T cell phenotypes in wild-type (WT) and Traf5-deficient (KO) mice fed a high-fat diet (HFD). Although lymphocyte composition was broadly comparable, KO mice showed reduced spontaneous immunoglobulin G2c (IgG2c) production ex vivo—about 1.5-fold lower than WT. Notably, despite elevated TNF-α and CD40 ligand (CD40L) expression in HFD-fed KO splenocytes, IgG2c production remained diminished—about 1.9-fold lower than WT—upon soluble CD40L stimulation, indicating impaired CD40-mediated class-switch recombination (CSR). Consistently, B cells from KO mice on a normal diet exhibited reduced activation-induced cytidine deaminase (AID) expression—about 4.4-fold lower than WT—after CD40L stimulation, and decreased IgG2c secretion—about 6.6-fold lower—upon CD40L and IFN-γ co-stimulation in vitro. Collectively, these findings suggest that TRAF5 is involved in CD40-dependent CSR in B cells under inflammatory conditions and may contribute to sustaining adaptive immune responses during obesity-associated chronic inflammation. Full article

(This article belongs to the Section Molecular Endocrinology and Metabolism)

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22 pages, 1489 KB

Open AccessReview

Antinuclear Antibodies in Polycystic Ovary Syndrome: A Systematic Review of Observational Studies

by Jakub Kwiatkowski, Nicole Akpang, Lucja Zaborowska and Artur Ludwin

Int. J. Mol. Sci. 2025, 26(19), 9493; https://doi.org/10.3390/ijms26199493 (registering DOI) - 28 Sep 2025

Abstract

Polycystic ovary syndrome (PCOS), the most common endocrine disorder in reproductive-age women, is characterized by menstrual irregularities and polycystic ovarian morphology. It is also associated with insulin resistance, chronic inflammation, and oxidative stress, all of which may promote autoimmunity. Several studies have suggested [...] Read more.

Polycystic ovary syndrome (PCOS), the most common endocrine disorder in reproductive-age women, is characterized by menstrual irregularities and polycystic ovarian morphology. It is also associated with insulin resistance, chronic inflammation, and oxidative stress, all of which may promote autoimmunity. Several studies have suggested a higher occurrence of antinuclear antibodies (ANA) in PCOS but the main challenge in this field is the inconsistency of findings due to heterogeneous study designs and assay methods. However, to date, no systematic review has synthesized this evidence. We conducted a systematic review to evaluate the prevalence and serum levels of ANA in women with PCOS. A comprehensive search was performed in PubMed, Embase, and Scopus, and 13 studies were ultimately included, comprising 924 women with PCOS and 1172 controls. ANA were elevated in about half of the studies, while the remainder found no significant differences between PCOS and controls. Anti-dsDNA antibodies were the most consistently investigated ANA subtype, with most studies reporting higher levels or prevalence in PCOS. For other ANA subtypes, the evidence was limited and inconclusive, largely due to methodological variability across studies. This systematic review suggests that ANA may be elevated in a subset of women with PCOS, but the current evidence remains inconsistent. These findings highlight the need for methodological standardization in ANA assessment to enable clearer conclusions and to clarify whether ANA positivity has clinical relevance in this population. Full article

(This article belongs to the Section Molecular Immunology)

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29 pages, 1113 KB

Open AccessReview

The Role of GABA Pathway Components in Pathogenesis of Neurodevelopmental Disorders

by Ekaterina V. Marilovtseva, Amal Abdurazakov, Artemiy O. Kurishev, Vera A. Mikhailova and Vera E. Golimbet

Int. J. Mol. Sci. 2025, 26(19), 9492; https://doi.org/10.3390/ijms26199492 (registering DOI) - 28 Sep 2025

Abstract

γ-aminobutyric acid (GABA), the primary inhibitory neurotransmitter in the central nervous system (CNS), regulates neuronal excitability, synaptic plasticity, and oscillatory activity essential for cognition, emotion, and behavior. Disruptions in GABAergic signaling are increasingly recognized as key contributors to a range of neurodevelopmental disorders [...] Read more.

γ-aminobutyric acid (GABA), the primary inhibitory neurotransmitter in the central nervous system (CNS), regulates neuronal excitability, synaptic plasticity, and oscillatory activity essential for cognition, emotion, and behavior. Disruptions in GABAergic signaling are increasingly recognized as key contributors to a range of neurodevelopmental disorders (NDDs), including schizophrenia (SZ), autism spectrum disorder (ASD), major depressive disorder (MDD), bipolar disorder (BD), and intellectual disability (ID). In this review, we analyze the data available from the literature concerning the components of the GABA pathway. We describe the main steps of GABA metabolism, including GABA synthesis and release, GABA receptors neurotransmission, GABA reuptake and catabolism, and evaluate their involvement in the pathogenesis of neurodevelopmental disorders. We suggest the possibility of existence of so far undescribed mechanisms which maintain the concentrations of GABA at a relatively physiological level when the function of glutamic acid decarboxylases is compromised by mutations. Searching for these mechanisms could be important for better understanding neurodevelopment and could give a clue for future searches for new therapeutic approaches for treating or alleviating the symptoms of BD and SZ. We also argue that the metabolic stage of the GABA pathway has only a minor direct effect on GABA signaling and rather causes clinical effects due to accumulation of neurotoxic byproducts. Full article

(This article belongs to the Special Issue Molecular Investigations in Neurodevelopmental Disorders)

13 pages, 2582 KB

Open AccessArticle

Unsupervised Machine Learning Reveals Temporal Components of Gene Expression in HeLa Cells Following Release from Cell Cycle Arrest

by Tom Maimon, Yaron Trink, Jacob Goldberger and Tomer Kalisky

Int. J. Mol. Sci. 2025, 26(19), 9491; https://doi.org/10.3390/ijms26199491 (registering DOI) - 28 Sep 2025

Abstract

Gene expression measurements of tissues, tumors, or cell lines taken over multiple time points are valuable for describing dynamic biological phenomena such as the response to growth factors. However, such phenomena typically involve multiple biological processes occurring in parallel, making it difficult to [...] Read more.

Gene expression measurements of tissues, tumors, or cell lines taken over multiple time points are valuable for describing dynamic biological phenomena such as the response to growth factors. However, such phenomena typically involve multiple biological processes occurring in parallel, making it difficult to identify and discern their respective contributions at any time point. Here, we demonstrate the use of unsupervised machine learning to deconvolve a series of time-dependent gene expression measurements into its underlying temporal components. We first downloaded publicly available RNAseq data obtained from synchronized HeLa cells at consecutive time points following release from cell cycle arrest. Then, we used Fourier analysis and Topic modeling to reveal three underlying components and their relative contributions at each time point. We identified two temporal components with oscillatory behavior, corresponding to the G1-S and G2-M phases of the cell cycle, and a third component with a transient expression pattern, associated with the immediate early response gene program, regulation of cell proliferation, and cervical cancer. This study demonstrates the use of unsupervised machine learning to identify hidden temporal components in biological systems, with potential applications to early detection and monitoring of diseases and recovery processes. Full article

(This article belongs to the Special Issue Molecular Mechanisms of mRNA Transcriptional Regulation: 3rd Edition)

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21 pages, 7472 KB

Open AccessArticle

Identification and Expression Analysis of CCCH Zinc Finger Proteins in Mulberry (Morus alba)

by Feng Chen, Jie Yu, Zhi-Hong Han and Yong-Jin Deng

Int. J. Mol. Sci. 2025, 26(19), 9490; https://doi.org/10.3390/ijms26199490 (registering DOI) - 28 Sep 2025

Abstract

CCCH zinc finger proteins play critical roles in plant growth, development and stress responses. Here, 56 CCCH genes were identified in Morus alba. These genes displayed wide variation in coding sequence (456–6318 bp) and protein length (151–2105 aa), with most proteins predicted [...] Read more.

CCCH zinc finger proteins play critical roles in plant growth, development and stress responses. Here, 56 CCCH genes were identified in Morus alba. These genes displayed wide variation in coding sequence (456–6318 bp) and protein length (151–2105 aa), with most proteins predicted to localize in the nucleus and a few in chloroplasts, the endoplasmic reticulum or cytoplasm. Chromosomal mapping showed uneven distribution across 14 chromosomes, with tandem clusters on chromosomes 1, 6 and 13. Phylogenetic analysis classified 53 MaC3Hs into 13 subfamilies, while three genes remained ungrouped. Synteny analysis revealed four segmental duplication events, suggesting segmental duplication as the major expansion mechanism, under purifying selection. Comparative collinearity showed higher conservation with Arabidopsis thaliana than with rice or maize. Promoter analysis identified 22 cis-acting elements, mainly related to phytohormones, followed by abiotic stress and developmental regulation. Expression profiling under drought stress revealed differential expression across tissues, with MaC3H33 showing strong induction (>200-fold in stems on day 6). Subcellular localization confirmed MaC3H33 is nuclear, and yeast assays indicated no self-activation. These findings provide comprehensive insights into the MaC3H gene family and lay a foundation for functional studies related to drought tolerance in mulberry. Full article

(This article belongs to the Section Molecular Plant Sciences)

23 pages, 712 KB

Open AccessArticle

Hormone Receptor Positive/HER2 Negative Breast Carcinoma: Association of PIK3CA Mutational Status with PD-L1 and Tumor Cell Microenvironment and Their Prognostic Significance

by Danijel Lopac, Emina Babarović, Justin Hagen, Petra Valković Zujić, Damir Grebić and Ita Hadžisejdić

Int. J. Mol. Sci. 2025, 26(19), 9489; https://doi.org/10.3390/ijms26199489 (registering DOI) - 28 Sep 2025

Abstract

Novel research data in different cancer types indicate that mutations within PIK3CA might serve as a biomarker of an improved response to immune therapy. Therefore, the aim of this study was to evaluate and examine possible differences in the tumor microenvironment composition and [...] Read more.

Novel research data in different cancer types indicate that mutations within PIK3CA might serve as a biomarker of an improved response to immune therapy. Therefore, the aim of this study was to evaluate and examine possible differences in the tumor microenvironment composition and PD-L1 expression as well the prognostic significance of CD4, CD8, CD68, and CD163 in PIK3CA mutated and non-mutated hormone receptor positive and HER2 negative (HR+/HER2-) breast carcinoma. Breast carcinoma tissue was analyzed by Cobas PIK3CA mutation test for the presence of PIK3CA mutation and immunohistochemistry was applied to assess PD-L1 expression and CD4, CD8, CD68, and CD163 infiltration within tumor. Statistically significant association was observed between PD-L1 expression and the presence of PIK3CA exon 20 mutation (p = 0.044), with PD-L1–positive patients predominantly harboring this mutation. Tumors harboring PIK3CA mutations exhibited moderate to strong statistically significant positive correlations between PD-L1 expression and infiltration by CD8 cells (rs = 0.462, p = 0.0027), CD68 cells (rs = 0.398, p = 0.0134), and CD163 cells (rs = 0.617, p < 0.0001). In patients with PIK3CA mutation and exon 20 PIK3CA mutation there was statistically significant longer survival without recurrence (p = 0.026 and p = 0.041, respectively). Research regarding PD-L1 expression, immune cells and PIK3CA mutations might have an impact on how to determine therapeutic approaches for patients with HR+/HER2- breast carcinoma. Full article

(This article belongs to the Special Issue Metabolic Dynamics and Immune Surveillance in the Tumor Microenvironment)

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