International Journal of Molecular Sciences

18 pages, 1006 KB

Open AccessArticle

Mechanistic Insights into Vernonia calvoana-Induced Apoptosis in Ovarian Cancer Cells via the Intrinsic Pathway

by Ariane M. Chitoh, Clement G. Yedjou, Ingrid K. Tchakoua, Sylvianne Njiki, Felicite K. Noubissi, Titilope Komolafe, Kayode Komolafe, Oluwatoyin V. Odubanjo and Paul B. Tchounwou

Int. J. Mol. Sci. 2026, 27(17), 7887; https://doi.org/10.3390/ijms27177887 - 3 Sep 2026

Abstract

Vernonia calvoana (VC), a commonly used medicinal plant in West Africa, has been shown by our research team to inhibit the proliferation of OVCAR-3 ovarian cancer cells through mechanisms involving oxidative stress, DNA damage, and S-phase cell cycle arrest. The objective of the [...] Read more.

Vernonia calvoana (VC), a commonly used medicinal plant in West Africa, has been shown by our research team to inhibit the proliferation of OVCAR-3 ovarian cancer cells through mechanisms involving oxidative stress, DNA damage, and S-phase cell cycle arrest. The objective of the current study was to elucidate the intrinsic apoptotic mechanisms triggered by VC fraction seven (VCF7). OVCAR-3 cells were treated with VCF7 (0, 8, 16, and 32 μg/mL) for a duration of 48 h. Apoptosis was assessed using Annexin V/Propidium Iodide (PI) staining followed by flow cytometry analysis. Mitochondrial membrane potential (ΔΨm) was assessed through JC-1 staining and confocal microscopy, while chromatin condensation was analyzed using DAPI staining. DNA fragmentation was examined by agarose gel electrophoresis. Caspase 3 activity was measured using flow cytometry. Protein expression levels of p53, Bcl-2, cytochrome c, caspase-9, and caspase-3 were determined by Western blot analysis, and mRNA expression levels of p53 and Bcl-2 were evaluated using qRT-PCR. VCF7 induced apoptosis in a concentration-dependent manner. Analysis using Annexin V/PI indicated an increase in apoptotic cell populations from 10.5% to 30%, along with a rise in necrotic cells from 7% to 50% across treatment concentrations. A modest, concentration-associated decrease in mitochondrial membrane potential was recorded (0.96-, 0.88-, and 0.85-fold at 8, 16, and 32 μg/mL, respectively; p < 0.05). DAPI staining validated the concentration-dependent chromatin condensation and nuclear fragmentation. The analysis of DNA fragmentation showed progressive internucleosomal degradation, appearing as a smear pattern with distinct fragments at elevated concentrations, indicative of concurrent apoptotic and necrotic cell death. The activation of caspase-3 reached a peak of 28% at 16 μg/mL. Western blot analysis indicated an upregulation of p53, a downregulation of Bcl-2, an increase in total cytochrome c protein levels, and an increased expression of caspase-9 and caspase-3 in a concentration-dependent manner. These findings were corroborated at the transcriptional level by qRT-PCR, which showed increased p53 mRNA and decreased Bcl-2 mRNA expression. Taken together, these results underscore the potential of VCF7 as a promising plant-derived anticancer agent and support the need for further preclinical and clinical studies in ovarian cancer. Full article

(This article belongs to the Special Issue Anticancer, Antioxidant, and Anti-Inflammatory Properties of Natural Products)

21 pages, 2646 KB

Open AccessArticle

Cross-Cohort Transcriptomic Prioritization and Chemical-Provenance Assessment of Asthma Airway-Brushing Genes Overlapping HERB-Annotated Scrophularia ningpoensis Targets

by Jinhao Zou, Xiaowei Tian, Siyi Wang and Ye Sun

Int. J. Mol. Sci. 2026, 27(17), 7886; https://doi.org/10.3390/ijms27177886 - 3 Sep 2026

Abstract

Direct human evidence linking Scrophularia ningpoensis to asthma is limited, and database-derived herb–target records do not establish constituent exposure or target engagement. We used an evidence-audited molecular-informatics workflow to prioritize asthma airway-brushing-associated genes overlapping a frozen HERB export. GSE63142 was the discovery set, [...] Read more.

Direct human evidence linking Scrophularia ningpoensis to asthma is limited, and database-derived herb–target records do not establish constituent exposure or target engagement. We used an evidence-audited molecular-informatics workflow to prioritize asthma airway-brushing-associated genes overlapping a frozen HERB export. GSE63142 was the discovery set, GSE67472 the independent airway-epithelial replication set, GSE137268 an induced-sputum cross-biospecimen transfer set, and GSE43696 a descriptive same-cohort reference because 105 of 108 identifiers overlapped GSE63142. Of 1266 measurable HERB-annotated targets, an 81-gene FDR-defined overlap did not exceed an expression-matched null (p = 0.0972), whereas a 19-gene strict overlap showed 2.27-fold enrichment (empirical p = 3.00 × 10⁻⁴) and 12 genes met the prespecified replication criterion in GSE67472. Provenance sensitivity retained two genes after database-mining-only edges were excluded and none under a direct-target-engagement requirement. Nested classifiers transferred to GSE67472, but not to sputum. Out-of-fold SHAP identified model-specific contributors, with moderate cross-cohort rank stability for LASSO (Spearman ρ = 0.563) and random forest (ρ = 0.693); SHAP was not interpreted as causal or herbal-target importance. These findings support computational prioritization and transferability assessment, not chemical presence, exposure, target binding, mechanism, or efficacy. Full article

(This article belongs to the Special Issue Molecular Crosstalk in Allergy, Barrier Dysfunction, and Asthma)

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32 pages, 1353 KB

Open AccessReview

Animal Models of Hyperoxaluria and Their Relevance for Fundamental Research and Clinical Practice

by Dominika Szkopek-Zaworska, Mariusz Strutyński, Janine Donaldson, Stefan Pierzynowski, Kateryna Pierzynowska and Tomasz Jacek

Int. J. Mol. Sci. 2026, 27(17), 7885; https://doi.org/10.3390/ijms27177885 - 3 Sep 2026

Abstract

In vivo models have been central to understanding hyperoxaluria pathogenesis and to the development of emerging therapeutic strategies, but no single model fully reproduces the complexity of human disease. This narrative review critically evaluates currently available in vivo models of hyperoxaluria and provides [...] Read more.

In vivo models have been central to understanding hyperoxaluria pathogenesis and to the development of emerging therapeutic strategies, but no single model fully reproduces the complexity of human disease. This narrative review critically evaluates currently available in vivo models of hyperoxaluria and provides a framework for their selection, interpretation, and integration according to the specific phenotype and biological or therapeutic question under investigation. A structured, non-systematic literature search was conducted in PubMed, Web of Science, Scopus, and Google Scholar, with emphasis on peer-reviewed primary studies and relevant reviews addressing experimental models, disease mechanisms, and therapeutic interventions. Chemically and dietary induced, genetic, enteric and microbial, and large-animal models were evaluated with respect to model validity, experimental endpoints, pathophysiological relevance, and translational potential. A central feature of this review is the distinction between related but non-interchangeable phenotypes, including hyperoxaluria, crystalluria, nephrocalcinosis, oxalate nephropathy, and nephrolithiasis. This distinction provides the conceptual basis for comparing models that reproduce different stages or consequences of oxalate exposure rather than treating all calcium oxalate-associated phenotypes as equivalent. Chemically induced models are particularly useful for studying hyperoxaluria, calcium oxalate crystallization, and acute or subacute renal injury, whereas genetic models reproduce specific molecular defects underlying primary hyperoxaluria and support the development of mechanism-based therapies. Enteric and microbial models address intestinal oxalate handling and the gut–kidney axis and are particularly relevant for investigating gut-directed therapeutic strategies. Naturally occurring models may provide complementary insight into chronic clinical phenotypes, whereas large-animal models can facilitate selected translational and experimentally intensive investigations. The reviewed evidence demonstrates that no model can be considered superior. Instead, model selection should be guided by the specific mechanism, phenotype, or therapeutic intervention under investigation. This review therefore proposes a phenotype-oriented and question-driven framework for model selection and interpretation, taking into consideration validity, reproducibility, ethical aspects, and the limits of translational extrapolation. Full article

(This article belongs to the Topic Animal Models of Human Disease 3.0)

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15 pages, 11022 KB

Open AccessArticle

Efficient Endolymphatic Sac-Directed Gene Delivery Using AAV8BP2 and Posterior Semicircular Canal Injection

by Minjin Kang, Michelle J. Suh, Heon Yung Gee, Wade W. Chien and Jinsei Jung

Int. J. Mol. Sci. 2026, 27(17), 7884; https://doi.org/10.3390/ijms27177884 - 3 Sep 2026

Abstract

Mutations in SLC26A4, which encodes the anion transporter pendrin, represent one of the most common genetic causes of hereditary hearing loss, including Pendred syndrome and DFNB4. Pendrin plays a critical role in maintaining ion homeostasis within the inner ear, particularly in the [...] Read more.

Mutations in SLC26A4, which encodes the anion transporter pendrin, represent one of the most common genetic causes of hereditary hearing loss, including Pendred syndrome and DFNB4. Pendrin plays a critical role in maintaining ion homeostasis within the inner ear, particularly in the endolymphatic sac (ES), making it an important therapeutic target for gene replacement strategies. However, efficient delivery of therapeutic genes to relevant inner ear structures remains a major challenge for clinical translation. In this study, we evaluated the inner ear transduction profile of AAV8BP2, an engineered AAV8-derived capsid, in comparison with AAV2.7m8 and AAV8 in mice. Neonatal mice received posterior semicircular canal (PSCC) injections at postnatal day 0 (P0), and viral transduction in the cochlea and ES was assessed at P7. To examine age-dependent differences in viral transduction, additional experiments were performed in adult mice injected at P21 and analyzed at P28. We also compared three surgical delivery routes for inner ear gene transfer: PSCC injection, round window membrane (RWM) injection, and RWM injection combined with PSCC fenestration. AAV8BP2 effectively transduced the ES in both neonatal and adult mice and showed greater GFP expression in the spiral prominence than AAV8 following neonatal administration. Among the three delivery routes evaluated in adult mice, PSCC injection achieved the highest ES transduction while maintaining cochlear hair cell transduction comparable to that achieved with RWM-based approaches. Together, these findings define the relative transduction profiles of the tested AAV capsids and delivery routes and provide a basis for selecting vector-delivery route combinations for SLC26A4-targeted inner ear gene therapy. Full article

(This article belongs to the Special Issue Hearing Loss: Molecular Biological Insights, 2nd Edition)

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15 pages, 1850 KB

Open AccessArticle

Investigation of the Protective Effect of Centella asiatica Against Doxorubicin-Induced Testicular Damage in Rats

by Fevzi Bedir, Zeynep Suleyman, Huseyin Kocaturk, Mehmet Sefa Altay, Ferda Keskin Cimen, Durdu Altuner, Mansura Babayeva and Halis Suleyman

Int. J. Mol. Sci. 2026, 27(17), 7883; https://doi.org/10.3390/ijms27177883 - 3 Sep 2026

Abstract

Doxorubicin (DOX) is an antineoplastic agent commonly used in cancer therapy that is known for its testicular toxicity. DOX-induced testicular injury involves inflammation, reactive oxygen species, and oxidative stress. Centella asiatica exhibits anti-inflammatory and antioxidant properties. The present experimental study aimed to determine [...] Read more.

Doxorubicin (DOX) is an antineoplastic agent commonly used in cancer therapy that is known for its testicular toxicity. DOX-induced testicular injury involves inflammation, reactive oxygen species, and oxidative stress. Centella asiatica exhibits anti-inflammatory and antioxidant properties. The present experimental study aimed to determine the potential protective efficacy of Centella asiatica in a rat model of doxorubicin-induced testicular toxicity. Rats were randomly assigned to four groups: healthy control (HC), CA, DOX, and CA + DOX (CADX). An oral dose of 200 mg/kg Centella asiatica was administered to the CA and CADX groups. The HC and DOX groups received saline. One hour later, DOX (7.5 mg/kg) was intraperitoneally injected into the DOX and CADX groups on days 1, 4, and 7. Centella asiatica markedly attenuated the DOX-induced increase in malondialdehyde, nitric oxide, and pro-inflammatory cytokine levels, while preventing the decrease in superoxide dismutase activity in testicular tissue (p < 0.001). Centella asiatica reduced the severity of DOX-induced morphological damage in testicular tissue (p < 0.05). Moreover, it partially restored reproductive hormone function. In conclusion, Centella asiatica demonstrates significant potential in mitigating DOX-induced oxidative damage, attenuating testicular injury and preserving the functional integrity of the male reproductive system. Full article

(This article belongs to the Section Bioactives and Nutraceuticals)

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22 pages, 22936 KB

Open AccessReview

The RNA-Binding Protein ELAVL4/HuD Promotes Stress-Associated Tumor Survival in Neuroendocrine Cancers

by Kausik Bishayee, Vaishak Kaviyarasan, Sun Young Yoo, Seung Hee Lee and Yong Soo Park

Int. J. Mol. Sci. 2026, 27(17), 7882; https://doi.org/10.3390/ijms27177882 - 3 Sep 2026

Abstract

Neuro-endocrine-related cancers overexpress ELAVL4 (HuD), a neuron-specific RBP implicated in post-transcriptional regulation. HuD plays a role in tumor cell survival; its knockdown in cancer cells and tumors leads to reduced growth and viability. In this review, we addressed HuD’s role in several molecular [...] Read more.

Neuro-endocrine-related cancers overexpress ELAVL4 (HuD), a neuron-specific RBP implicated in post-transcriptional regulation. HuD plays a role in tumor cell survival; its knockdown in cancer cells and tumors leads to reduced growth and viability. In this review, we addressed HuD’s role in several molecular pathways that contribute to the development of cancer. For example, cancer cells that have high levels of HuD are able to better withstand stressful tumor microenvironments because HuD stabilizes certain mRNAs, which promotes tumor development, modulates oxidative and metabolic stress, enhances autophagy, and impairs apoptosis. We discussed future studies on HuD in cancer, which should focus on its diverse roles in various cancer types and the molecular aspects. Furthermore, assessing HuD’s contribution to the efficacy of immunotherapy requires an understanding of how it affects immune responses in malignancies. The development of targeted therapies, such as RNA-based approaches and small molecules, offers intriguing avenues for precision cancer management. The transition of HuD-directed therapies from preclinical models to clinical trials is anticipated to be accelerated by ongoing advancements in RNA-targeted drug discovery, structural biology, medicinal chemistry, and targeted drug delivery, even though no HuD-specific therapies have yet entered standard clinical practice. Full article

(This article belongs to the Special Issue Targeted Cancer Therapeutics: Molecular Pathways and Precision Strategies)

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15 pages, 8644 KB

Open AccessArticle

Microbial-Derived Daidzin (Eco-3) Suppresses RANKL-Induced Osteoclastogenesis by Targeting the TBK1–NFATc1 Signaling Axis

by Nivethasri Lakshmana Perumal, Kyung-Bon Koo, Gi-Young Park and Byeong-Churl Jang

Int. J. Mol. Sci. 2026, 27(17), 7881; https://doi.org/10.3390/ijms27177881 - 3 Sep 2026

Abstract

Eco-3, a microbial-derived daidzin, has been reported to possess diverse biological activities; however, its effects on osteoclast differentiation and the underlying molecular mechanisms remain unclear. In the present study, we investigated the effects of Eco-3 on receptor activator of nuclear factor-κB ligand (RANKL)-induced [...] Read more.

Eco-3, a microbial-derived daidzin, has been reported to possess diverse biological activities; however, its effects on osteoclast differentiation and the underlying molecular mechanisms remain unclear. In the present study, we investigated the effects of Eco-3 on receptor activator of nuclear factor-κB ligand (RANKL)-induced osteoclastogenesis and explored the signaling pathways involved using RAW264.7 macrophages. Eco-3 suppressed RANKL-induced osteoclast formation at the concentrations tested without significantly affecting cell viability. Eco-3 also altered F-actin organization and reduced the expression of key osteoclastogenic markers, including tartrate-resistant acid phosphatase (TRAP), nuclear factor of activated T cells c1 (NFATc1), c-Fos, and cathepsin K (CTSK). In particular, Eco-3 attenuated NFATc1 expression during the early stage of osteoclast differentiation, suggesting interference with the transcriptional program associated with osteoclastogenesis. Furthermore, RANKL stimulation progressively increased TANK-binding kinase 1 (TBK1) phosphorylation during osteoclast differentiation, whereas Eco-3 attenuated this activation. Genetic silencing of TBK1 suppressed osteoclast formation, while pharmacological inhibition of TBK1 reduced TBK1 phosphorylation, osteoclastogenic gene expression, and osteoclast formation. Collectively, these findings suggest that Eco-3 suppresses RANKL-induced osteoclastogenesis, at least in part, through modulation of the TBK1–NFATc1 signaling axis in RAW264.7 macrophages. Our findings identify TBK1 as a potential regulatory component of osteoclast differentiation and suggest that Eco-3 warrants further investigation as a potential bioactive candidate for osteoclast-related bone disorders. Full article

(This article belongs to the Special Issue Bone and Cartilage Injury and Repair: Molecular Aspects)

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19 pages, 25977 KB

Open AccessArticle

Microparticles Expressing IL-1β Are Linked to Neuroinflammation and Cognitive Decline After Carbon Monoxide Poisoning

by Awadhesh K. Arya, Kinjal Sethuraman, Jaylyn Waddell, Abid R. Bhat, Zuha Imtiyaz, Deepa Walia, Yuanyuan Liang, Yong Sung Cha, Yoonsuk Lee, Siamak Moayedi, Douglas Sward and Stephen R. Thom

Int. J. Mol. Sci. 2026, 27(17), 7880; https://doi.org/10.3390/ijms27177880 - 3 Sep 2026

Abstract

Immune mediators are elevated due to carbon monoxide (CO) poisoning but their role in the development of neurological deficits is unknown. Circulating microparticles (MPs) are elevated in response to CO and correlate with the development of neurological complications. We hypothesized that interleukin (IL)-1β [...] Read more.

Immune mediators are elevated due to carbon monoxide (CO) poisoning but their role in the development of neurological deficits is unknown. Circulating microparticles (MPs) are elevated in response to CO and correlate with the development of neurological complications. We hypothesized that interleukin (IL)-1β is carried by MPs and contributes to the development of neurological sequelae (NS). Blood-borne IL-1β in CO-poisoned patients is almost exclusively carried by MPs. Healthy humans have 0.8 ± 0.8 (n = 27) MPs/μL bearing IL-1β on the membrane surface. IL-1β-bearing MPs obtained from patients at the time of CO poisoning diagnosis who recover (Global Deterioration Score [GDS] = 1 at 1 month) numbered 35 ± 12/μL (n = 27, p < 0.001 vs. control) and patients who sustained NS (GDS > 1 at 1 month) had 75 ± 38/μL (n = 27; p < 0.001 vs. control and CO-recovered groups). Twice as many MPs carry IL-1β cargo as express surface-bearing IL-1β. The concentration is higher post-CO but does not correlate with NS. Those with NS have 43.8 ± 42.0 pg IL-1β /10⁶ MPs, and those with GDS = 1 have 33.0 ± 32.0 pg/10⁶ MPs, versus controls 5.4 ± 0.3 pg/10⁶ MPs, p < 0.001. In a murine CO model, MPs IL-1β cargo follows similar proportions to humans. Pharmacologic blockade of IL-1β using an IL-1 receptor antagonist or neutralizing anti-IL-1β antibody inhibited neuroinflammation and preserved neurological function. Results demonstrate that brain-derived MPs liberated via the glymphatic system to the peripheral circulation activate neutrophils which are the prime generators of IL-1β-bearing MPs that maintain a cycle of neuroinflammation. Targeting IL-1β disrupts MP-mediated inflammation. Full article

(This article belongs to the Special Issue Molecular Mechanism and Pharmacological Target of Neuroprotection)

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22 pages, 8696 KB

Open AccessArticle

Genome-Wide Identification and Bioinformatics Analysis of the FAD Gene Family in Walnut (Juglans regia L.)

by Fan Hao, Jingchuan Xia, Zhenlin Shen and Shuoxin Zhang

Int. J. Mol. Sci. 2026, 27(17), 7879; https://doi.org/10.3390/ijms27177879 - 3 Sep 2026

Abstract

Fatty acid desaturase (FAD) is a core catalytic enzyme in plants for the synthesis of unsaturated fatty acids, profoundly affecting plant growth, development, and adaptability to various environmental stresses. The walnut (Juglans regia L.) is an important woody oil tree [...] Read more.

Fatty acid desaturase (FAD) is a core catalytic enzyme in plants for the synthesis of unsaturated fatty acids, profoundly affecting plant growth, development, and adaptability to various environmental stresses. The walnut (Juglans regia L.) is an important woody oil tree species, and its kernel is rich in unsaturated fatty acids. Systematic identification of the walnut FAD gene family and analysis of its function are of great significance for revealing the molecular mechanisms underlying unsaturated fatty acid metabolism in the walnut. Based on walnut whole-genome data, this study used homology alignment and hidden Markov model search methods to identify the JrFAD gene family members. Subsequently, a variety of bioinformatics tools were used to systematically analyze their structural characteristics, evolutionary expansion mechanism, expression regulation, and function. A total of 21 JrFAD gene family members were identified and classified into five subfamilies. The family genes were unevenly distributed on nine chromosomes. WGD/segmental duplication was the main expansion method, and the duplicated gene pairs experienced strong purification selection. The family gene promoter sequence is rich in regulatory elements that respond to light, plant hormones, and various stresses. The expression pattern analysis showed that JrFAD3.1 and JrFAD2.3 showed high expression specifically during the rapid accumulation of walnut kernel oil. This study clarified the composition and evolutionary characteristics of the FAD gene family in the walnut, which provides useful information for in-depth analyses of its functional mechanism in the regulation of lipid metabolism, and also identified potential candidate gene resources for the genetic improvement of walnut varieties with high amounts of unsaturated fatty acids. Full article

(This article belongs to the Special Issue Plant Molecular Ecology and Genomic Perspectives)

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15 pages, 1096 KB

Open AccessArticle

Association Between Biopsy PD-L1 Combined Positive Score and Pathological Upgrading at Radical Prostatectomy in Grade Group 1 Prostate Cancer: A Retrospective Study

by Ludovica Pepe, Valeria Zuccalà, Ida Rizzuto, Walter Giuseppe Giordano, Mariagiovanna Ballato, Pietro Tralongo, Gabriele Ricciardi, Vincenzo Cianci, Marta Rossanese, Giuseppe Iatì, Silvana Parisi, Francesco Pierconti, Antonio Ieni, Guido Fadda, Pietro Pepe, Maurizio Martini and Vincenzo Fiorentino

Int. J. Mol. Sci. 2026, 27(17), 7878; https://doi.org/10.3390/ijms27177878 - 3 Sep 2026

Abstract

Programmed death-ligand 1 (PD-L1) expression in Grade Group 1 (GG1) prostate carcinoma biopsies has not been established as a marker of pathological upgrading at radical prostatectomy (RP). This two-center retrospective case–control study included 172 men with GG1 carcinoma in the biopsy closest to [...] Read more.

Programmed death-ligand 1 (PD-L1) expression in Grade Group 1 (GG1) prostate carcinoma biopsies has not been established as a marker of pathological upgrading at radical prostatectomy (RP). This two-center retrospective case–control study included 172 men with GG1 carcinoma in the biopsy closest to RP: all 86 patients upgraded to GG2 and 86 randomly selected non-upgraded controls from 126 eligible GG1 patients. PD-L1 was assessed with the SP263 clone using the combined positive score (CPS), with CPS ≥ 1 predefined before outcome comparison. CPS ≥ 1 occurred in 36/86 upgraded cases (41.9%) and 18/86 controls (20.9%; unadjusted odds ratio [OR], 2.72; 95% confidence interval [CI], 1.39–5.33; p = 0.005). After adjustment for serum prostate-specific antigen, positive-core count, Prostate Imaging Reporting and Data System category, and center, CPS ≥ 1 remained associated with upgrading (adjusted OR, 2.91; 95% CI, 1.47–5.97; p = 0.003). A Firth bias-reduced sensitivity model including digital rectal examination yielded a similar CPS estimate. Biopsy CPS ≥ 1 was associated with biopsy–RP grade discordance, but the study does not establish an optimal cutoff, predictive performance, or clinical utility. Prospective multicenter validation, including active-surveillance outcomes, is required. Full article

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

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23 pages, 3518 KB

Open AccessReview

Polyphenols as Multi-Target Regulators of Oxidative Stress, Mitochondrial Function, and Cell Survival Signaling in Skin Diseases

by Moon-Kyun Cho, Min Hyuk Choi, Ki Dam Kim, Sukh Que Park, Sang-Han Lee, Hae-Seon Nam and Yoon-Jin Lee

Int. J. Mol. Sci. 2026, 27(17), 7877; https://doi.org/10.3390/ijms27177877 - 3 Sep 2026

Abstract

Bioactive polyphenols have emerged as multi-target regulators of cellular processes involved in the pathogenesis of skin diseases. Skin disorders, including inflammatory conditions, photoaging, and skin cancers, are characterized by complex pathogenic mechanisms associated with oxidative stress, mitochondrial dysfunction, dysregulated signaling pathways, and metabolic [...] Read more.

Bioactive polyphenols have emerged as multi-target regulators of cellular processes involved in the pathogenesis of skin diseases. Skin disorders, including inflammatory conditions, photoaging, and skin cancers, are characterized by complex pathogenic mechanisms associated with oxidative stress, mitochondrial dysfunction, dysregulated signaling pathways, and metabolic imbalance. Excessive production of reactive oxygen species (ROS) and persistent inflammatory signaling contribute to disease progression and cellular adaptation under stress conditions. Unlike conventional agents that typically target a single pathway, polyphenols act on interconnected signaling and metabolic networks. These compounds regulate key signaling pathways, including phosphoinositide 3-kinase/protein kinase B (PI3K/Akt), mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK), AMP-activated protein kinase (AMPK), nuclear factor-κB (NF-κB), and nuclear factor erythroid 2-related factor 2 (Nrf2), thereby regulating cell survival, proliferation, inflammatory responses, antioxidant defense, and metabolic adaptation. Polyphenols also influence mitochondrial function by maintaining redox homeostasis, regulating energy metabolism, and affecting apoptosis-related signaling pathways. This review provides a mechanistic overview of the effects of polyphenols on oxidative stress, mitochondrial function, and cell survival signaling in skin diseases. In addition, the therapeutic implications and current limitations of polyphenol-based approaches are discussed, with particular emphasis on the translational gap between experimental findings and physiological relevance. Factors such as concentration, bioavailability, and cellular microenvironment are highlighted as major determinants of polyphenol activity and key challenges for clinical translation. Finally, the need for further in vivo and clinical investigations is emphasized to support the development of effective polyphenol-based therapeutic strategies for skin diseases. Full article

(This article belongs to the Special Issue Molecular Studies of Skin Diseases: From Mechanisms to Therapy)

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24 pages, 3098 KB

Open AccessArticle

Detoxifying Effects of a Phenolic-Rich Thunbergia laurifolia Water Extract Against Chlorpyrifos-Induced Oxidative Stress: Evidence from an Integrated In Vitro and In Vivo Study

by Phraepakaporn Kunnaja, Supaporn Intatham, Parirat Khonsung, Kanjana Jaijoy, Thunyatorn Yimsoo, Piyanuch Rojsanga and Seewaboon Sireeratawong

Int. J. Mol. Sci. 2026, 27(17), 7876; https://doi.org/10.3390/ijms27177876 - 3 Sep 2026

Abstract

Thunbergia laurifolia has long been used in traditional medicine for detoxification; however, the biological basis of its detoxifying effects remains poorly understood. This study investigated the detoxifying effects of a phenolic-rich aqueous extract of T. laurifolia using integrated in vitro and in vivo [...] Read more.

Thunbergia laurifolia has long been used in traditional medicine for detoxification; however, the biological basis of its detoxifying effects remains poorly understood. This study investigated the detoxifying effects of a phenolic-rich aqueous extract of T. laurifolia using integrated in vitro and in vivo approaches. Caffeic acid (CA) and rosmarinic acid (RA) were used as marker compounds for extract standardization. The aqueous extract was evaluated for antioxidant, acetylcholinesterase, and apoptosis-modulating activities in vitro, followed by evaluation in a chlorpyrifos-induced oxidative stress model in vivo. The extract exhibited antioxidant activity and maintained acetylcholinesterase (AChE) activity. In LX-2 hepatic stellate cells, the extract induced predominantly early apoptosis, whereas CA and RA induced predominantly late apoptosis. In chlorpyrifos-exposed rats, the extract restored AChE activity, reduced lipid peroxidation, and enhanced endogenous antioxidant defenses, as evidenced by decreased malondialdehyde (MDA) levels and increased glutathione (GSH) levels and superoxide dismutase (SOD) activity. Collectively, these findings suggest that attenuation of oxidative stress may represent one of the mechanisms underlying the detoxifying effects traditionally attributed to T. laurifolia. Full article

(This article belongs to the Special Issue Phytochemicals and Antioxidants in Health and Disease Modulation)

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15 pages, 3053 KB

Open AccessArticle

Berberine Inhibits Eczematous Skin S. aureus-Induced Mast Cell/Basophil Activation and Modulates MAPK-Associated Gene Expression

by Anish R. Maskey, Daniel Kopulos, Madison Spears, Zhen-Zhen Wang, Xian Mo, Ibrahim Musa, Nan Yang, Anna Nowak-Wegrzyn, Danna Chung, Anne L. Maitland, Julie Wang, Raj K. Tiwari, Hugh A. Sampson, Jan Geliebter and Xiu-Min Li

Int. J. Mol. Sci. 2026, 27(17), 7875; https://doi.org/10.3390/ijms27177875 - 3 Sep 2026

Abstract

Staphylococcus aureus (S. aureus), a primary exacerbating factor in eczema, remains a prevalent pathogenic public-health threat. The mechanism of mast cell/basophil degranulation in the context of S. aureus-exacerbated eczema remains unclear. We sought to investigate the direct effect of mast [...] Read more.

Staphylococcus aureus (S. aureus), a primary exacerbating factor in eczema, remains a prevalent pathogenic public-health threat. The mechanism of mast cell/basophil degranulation in the context of S. aureus-exacerbated eczema remains unclear. We sought to investigate the direct effect of mast cell/basophil activation by S. aureus isolated from patients with severe eczema undergoing topical steroid withdrawal (TSW) and understand the mechanism of berberine (BBR) in inhibiting this activation. Clinical S. aureus strains (N = 8) were isolated from skin swabs of severe eczema patients and confirmed by sequencing. Human basophils (KU812), rat basophils (RBL-2H3) and murine mast cells (MC/9) were pre-treated with BBR for 48 h. and stimulated with heat-killed standard S. aureus- and clinical strains for 45 min, and degranulation was measured. BBR’s molecular-targets on basophils were identified by computational modeling and validated by qRT-PCR. BBR prevented degranulation following standard S. aureus stimulation in KU812, RBL-2H3 and MC/9 cells. BBR dose-dependently inhibited degranulation in KU812. BBR inhibited TNF-α and IL-4 release, and markedly suppressed the expression of FcεR1 (α, β, γ), TNFα, MAPK1, MAPK3, AKT2, CASP9, and CCND1 following standard S. aureus stimulation. BBR dose-dependently inhibited KU812 cell degranulation, markedly reduced TNF-α, IL-4, and MAPK1 and enhanced NFκB1A expression following clinical S. aureus strain stimulation. BBR inhibition of S. aureus-induced KU812 activation was at least associated with inhibition of MAPK-associated gene expression. This study provides novel insights into BBR’s effect in preventing S. aureus and human basophil interaction. Full article

(This article belongs to the Special Issue Allergic Reactions and Immune Factors)

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21 pages, 6332 KB

Open AccessArticle

Drug Design Studio (DDS) 2.0: A Unified Platform for Network Pharmacology Integrated with Docking and Virtual Screening Workflow for Covalent/Non-Covalent Binders

by Mahmoud E. Soliman

Int. J. Mol. Sci. 2026, 27(17), 7874; https://doi.org/10.3390/ijms27177874 - 3 Sep 2026

Abstract

Network pharmacology has become a central paradigm in modern drug discovery, replacing the reductionist “one drug, one target” view with a systems-level understanding of how compounds engage networks of proteins that are linked to disease. Despite its impact, a typical network-pharmacology study remains [...] Read more.

Network pharmacology has become a central paradigm in modern drug discovery, replacing the reductionist “one drug, one target” view with a systems-level understanding of how compounds engage networks of proteins that are linked to disease. Despite its impact, a typical network-pharmacology study remains fragmented and technically demanding: researchers must query several independent databases, install and reconcile multiple standalone tools for target collection, network construction, hub-gene ranking and pathway enrichment, and then manually bridge the results into structure-based follow-up such as molecular docking. This fragmentation is a persistent barrier, particularly for experimental and non-specialist users. Here, we present the network-pharmacology module of Drug Design Studio (DDS) 2.0, a unified, user-friendly platform that streamlines the entire workflow—disease target retrieval, compound–target prediction, shared-target identification, protein–protein interaction (PPI) network construction, hub-gene ranking and Gene Ontology/pathway enrichment—within a single guided interface, consolidating steps that otherwise require several separate tools. Crucially, DDS 2.0 links the resulting hub genes directly to the docking and virtual-screening engine introduced in the previous DDS releases: representative experimental structures and mutant forms—for instance, resistance-conferring variants found in drug-resistant strains—of the target proteins are selected and streamed into a docking-ready workspace, with dedicated support for covalent binders. We validate the module against four independent published network-pharmacology studies spanning diverse diseases; DDS reproduces the reported hub genes with a mean recovery (recall) of 0.85 (range 0.80–0.90) and a mean Jaccard index of 0.74, and recovers the corresponding target sets and enriched pathways. DDS 2.0 thus delivers an integrated route from systems-level analysis to structure-based drug design. DDS 2.0 is freely and publicly accessible. Comprehensive user documentation is built directly into DDS and can be accessed at any time from the Documentation panel. Full article

(This article belongs to the Section Molecular Informatics)

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25 pages, 3595 KB

Open AccessArticle

Two Bacillus PGPB Strains in Wheat and Soybean: Wheat Growth Promotion Without Detectable Rhizosphere Microbiome Restructuring

by Elena Nikolaevna Voronina, Ekaterina Alexeevna Sokolova, Irina Nikolaevna Tromenschleger, Olga Viktorovna Mishukova, Valeria Aleksandrovna Fedorets, Inna Viktorovna Khlistun, Oleg Aleksandrovich Savenkov, Oleg Igorevich Saprikin, Maria Dmitrievna Buyanova, Irina Mikhailovna Filippova, Marina Andreevna Glukhova, Evgeny Ivanovich Rogaev, Lada Vladimirovna Zhohova, Andrey Dmitrievich Manakhov and Natalya Valentinovna Smirnova

Int. J. Mol. Sci. 2026, 27(17), 7873; https://doi.org/10.3390/ijms27177873 - 3 Sep 2026

Abstract

Plant growth-promoting bacteria (PGPB) are increasingly deployed as biofertilizers, yet the link between an inoculant’s genomic potential and its realized effect on the plant is rarely assessed within an integrative framework that jointly captures the rhizosphere microbiome, plant phenotype, and strain genome. Two [...] Read more.

Plant growth-promoting bacteria (PGPB) are increasingly deployed as biofertilizers, yet the link between an inoculant’s genomic potential and its realized effect on the plant is rarely assessed within an integrative framework that jointly captures the rhizosphere microbiome, plant phenotype, and strain genome. Two Bacillus strains—B. halotolerans 1453 and B. pumilus 630—were applied to wheat and soybean in a factorial pot experiment (2 strains × 2 application methods × 3 frequencies + control, 3–4 replicates). Rhizosphere samples (n = 67 after filtering) were profiled by 16S rRNA sequencing with PICRUSt2 functional prediction and compositional validation (Aitchison PERMANOVA, ALDEx2, ANCOM-BC2). The PGPB gene repertoire was characterized by genome mining (481 marker genes, 14 categories). Wheat phenotype (six traits) and soybean height were analyzed with models appropriate for count data (Negative Binomial and binomial GLMs) for treatment-vs.-control comparisons, and with factorial ANOVA for decomposition into main effects and interactions. Crop identity was the dominant factor shaping both microbiome structure and function (PERMANOVA R² = 14.7% taxonomically and R² = 7.8% functionally, both p < 0.001), with biologically meaningful taxonomic differences between wheat and soybean; strain, application count and method had no significant effect on community composition (R² < 4% each), and co-occurrence networks showed no reliable differences between crops once read depth and sample size were controlled for. Despite this neutrality at the microbiome level, inoculation significantly increased wheat spike count (NB-GLM, all 12 treatments vs. control, padj 0.0002–0.031), ear weight, and stem count, with application count the strongest source of variability and a pronounced strain × application count. Strain 1453 outperformed 630 in spike count (+23.1%, p = 0.012) and ear weight (+20.4%, p = 0.023); we hypothesize that this may be related to its more complete DNRA pathway (narGHI + nirB-nirD) and biocontrol genes (bacE, srfAA). Strain 630 produced a less pronounced effect than strain 1453 but was subject to smaller fluctuations across replicates (CV ≈ 16–21% vs. ≈24–26% for 1453), which may reflect better resilience to environmental fluctuations, possibly due to its confirmed rsbV/rsbW stress-tolerance regulon. Rhizosphere microbiome composition differed clearly by crop (wheat vs. soybean) but showed no detectable response to strain, application method, or application count. Despite this lack of a microbiome signal, inoculation significantly increased wheat spike count and ear weight, with the magnitude and stability of this effect differing by strain. We hypothesize that this strain-dependent difference relates to underlying genomic differences—particularly in nitrogen metabolism (DNRA pathway) and stress-tolerance genes—though this link has not been tested directly and remains a hypothesis for future work. Full article

(This article belongs to the Special Issue Recent Advances in Plant–Microbe Interactions)

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14 pages, 1623 KB

Open AccessReview

Myeloid-Derived Suppressor Cells (MDSCs) in Cardiovascular Risk of Obesity-Associated Diabetes

by Rocío Flores-Campos, Lourdes Hontecillas-Prieto, Daniel J. García-Domínguez, Antonio Fernández-Suárez, Iker Egusquiza-Lasuen, Antonio Pérez, Josep Ribalta, Juan Pedro-Botet, Víctor Sánchez-Margalet, on behalf of the Immunology Group of the Spanish Society of Laboratory Medicine (SEMEDLAB) and the Cardiovascular Disease Group of the Spanish Diabetes Society (SED)

Int. J. Mol. Sci. 2026, 27(17), 7872; https://doi.org/10.3390/ijms27177872 - 3 Sep 2026

Abstract

The dysregulation of immune homeostasis and the persistence of chronic, low-grade inflammation represent core pathophysiological drivers governing the onset and progression of metabolic and cardiovascular disorders. Myeloid-derived suppressor cells (MDSCs) comprise a highly heterogeneous population of immature myeloid cells that are rapidly mobilized [...] Read more.

The dysregulation of immune homeostasis and the persistence of chronic, low-grade inflammation represent core pathophysiological drivers governing the onset and progression of metabolic and cardiovascular disorders. Myeloid-derived suppressor cells (MDSCs) comprise a highly heterogeneous population of immature myeloid cells that are rapidly mobilized from the bone marrow in response to biological stressors, such as sustained tissue injury and chronic inflammatory signaling. Historically evaluated within oncology and infectious disease frameworks, accumulating evidence highlights the pivotal, context-dependent roles of MDSCs in cardiometabolic environments. In conditions of obesity and type 2 diabetes (T2D), MDSCs undergo substantial expansion and accumulation within peripheral tissues, including adipose tissue and the liver. Functionally, MDSCs act as dynamic immunoregulators that can either buffer metabolic inflammation, via the secretion of interleukin-10 (IL-10), transforming growth factor-beta (TGF-β), and nitric oxide (NO) or, conversely, reflect and exacerbate disease progression depending on specific cellular subsets, glycemic control, and tissue localization. Within the vascular system, specific monocytic MDSC subsets demonstrate significant atheroprotective and cardioprotective capabilities by dampening Th1/Th17-mediated arterial wall inflammation, stabilizing atherosclerotic plaques, and preserving cardiac structural architecture during heart failure. However, phenotypic and functional heterogeneity poses a critical clinical challenge, as certain persistent or altered subsets correlate with heightened cardiovascular risk and adverse cerebrovascular outcomes. This review delivers a comprehensive synthesis of contemporary insights into MDSC biology at the intersection of obesity-associated diabetes and cardiovascular disease, characterizing their dualistic mechanisms, distinguishing preclinical causal mechanisms from human observational data. Moreover, we have established a comprehensive framework to reconcile the conflicting protective versus detrimental effects of MDSCs. And finally, we have also evaluated their potential clinical utility as candidate biomarkers, delineating the safety imperatives essential for translating MDSC-targeted therapeutic interventions into clinical practice. Full article

(This article belongs to the Special Issue Molecular Metabolism in Human Health and Disease)

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18 pages, 4863 KB

Open AccessArticle

Jaceidin Inhibits Proliferation and Promotes Apoptosis in Oral Squamous Cell Carcinoma Cells by Regulating Survivin and AKT/ERK Signaling Pathways

by Ming-Ju Hsieh, Hsin-Yu Ho, Chia-Chieh Lin, Min-Yun Kao, Yu-Sheng Lo, Yi-Ching Chuang, Bharath Kumar Velmurugan and Mu-Kuan Chen

Int. J. Mol. Sci. 2026, 27(17), 7871; https://doi.org/10.3390/ijms27177871 - 3 Sep 2026

Abstract

Oral squamous cell carcinoma (OSCC) remains a clinically challenging malignancy because of recurrence, treatment resistance, and limited therapeutic efficacy in advanced disease. This study investigated the anticancer effects and molecular mechanisms of jaceidin (JAC), a naturally occurring flavonoid derivative, in human OSCC cells. [...] Read more.

Oral squamous cell carcinoma (OSCC) remains a clinically challenging malignancy because of recurrence, treatment resistance, and limited therapeutic efficacy in advanced disease. This study investigated the anticancer effects and molecular mechanisms of jaceidin (JAC), a naturally occurring flavonoid derivative, in human OSCC cells. SCC-1 and SCC-47 cells were treated with JAC, and cell viability, colony formation, cell cycle distribution, apoptosis, and apoptosis-related signaling pathways were examined. JAC reduced OSCC cell viability and colony formation in a dose- and time-dependent manner. It also induced G2/M cell cycle accumulation and decreased the expression of cyclin D1, cyclin E1, phosphorylated cdc2, and CDK2/4/6. Apoptosis analyses showed that JAC promoted caspase-dependent apoptotic signaling, as evidenced by increased cleavage of caspase-3, caspase-8, caspase-9, and PARP. JAC modulated death receptor-associated signaling, characterized by increased Fas, TRADD, and DR5 expression and caspase-8 cleavage, while the decoy receptors DcR2 and DcR3 were also upregulated. JAC also promoted mitochondrial apoptotic signaling by increasing Bax, Bak, and Bim expression while decreasing Mcl-1. In addition, JAC attenuated AKT and ERK1/2 phosphorylation, and pharmacological inhibition with LY294002 or U0126 further enhanced JAC-induced apoptotic signaling. Furthermore, JAC reduced survivin expression and attenuated survivin-mediated apoptotic resistance. These findings suggest that JAC suppresses OSCC cell survival in association with modulation of AKT/ERK–survivin signaling and caspase-dependent apoptosis. Full article

(This article belongs to the Special Issue Molecular Diagnosis and Treatment of Oral Cancer)

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17 pages, 1516 KB

Open AccessBrief Report

Let-7a-5p/SHIP-1 Axis Drives SARS-CoV-2 Spike-1-Induced Microglial Pyroptosis

by Puja Pawar, Shraddha Ratnakar and Vandana Saxena

Int. J. Mol. Sci. 2026, 27(17), 7870; https://doi.org/10.3390/ijms27177870 - 3 Sep 2026

Abstract

Although persistent neurological sequelae in long COVID are reportedly well associated with neuroinflammation, the underlying regulatory mechanisms remain poorly characterized. Previously, we identified dysregulated microRNA expression, including let-7a-5p, in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike S1-stimulated human microglial cells by RNA [...] Read more.

Although persistent neurological sequelae in long COVID are reportedly well associated with neuroinflammation, the underlying regulatory mechanisms remain poorly characterized. Previously, we identified dysregulated microRNA expression, including let-7a-5p, in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike S1-stimulated human microglial cells by RNA sequencing; however, how let-7a-5p regulates the S1-mediated neuroinflammatory processes remains undetermined. In the present study, we examined the functional role of let-7a-5p in alleviating S1-induced microglial inflammation in the CHME3 cell line as well as in human monocyte-derived microglia (MDMi) using a loss- and gain-of-function approach. Functional inhibition of let-7a-5p resulted in mitigating S1-induced inflammatory cytokine release and markers of pyroptosis. Mechanistically, we established SHIP-1 as a direct target of let-7a-5p using luciferase reporter assay validation. Interestingly, we noted upregulated expression of the TLR3 gene alongside TLR2/4 in S1-stimulated microglia. Although we could not establish exactly how TLR3 is stimulated in S1-induced neuroinflammatory processes, using siRNA-mediated inhibition and a pharmacological inhibitor in both CHME3 cells and MDMi, our study certainly provides evidence of TLR3 involvement during S1-induced microglial inflammation, which needs further investigation. Together, these in vitro findings demonstrate that the let-7a-5p/SHIP-1 axis regulates S1-induced inflammatory cascades in CHME3 and MDMi cells, providing mechanistic insight into its role in SARS-CoV-2-associated neuroinflammation and warranting further validation in appropriate in vivo/organoid models. Full article

(This article belongs to the Section Molecular Biology)

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12 pages, 14271 KB

Open AccessArticle

HIF-PH Inhibitor Promotes Stabilization of HIF-1α via Inhibition of Its Degradation and Exerts Chondroprotective Effects in a Rat Osteoarthritis Model

by Kei Nakamura, Yuta Fujii, Yuji Arai, Shuji Nakagawa, Atsuo Inoue, Ryota Cha, Keisuke Sugie, Kentaro Hayashi, Tomoki Saito, Tsunao Kishida, Osam Mazda and Kenji Takahashi

Int. J. Mol. Sci. 2026, 27(17), 7869; https://doi.org/10.3390/ijms27177869 - 3 Sep 2026

Abstract

Articular cartilage exists under hypoxic conditions, where hypoxia-inducible factor (HIF)-1α plays a critical role in maintaining its homeostasis. In osteoarthritis (OA), however, this hypoxic environment is disrupted, and decreased HIF-1α expression contributes to disease progression. HIF-prolyl hydroxylase (HIF-PH) inhibitors stabilize HIF-1α and are [...] Read more.

Articular cartilage exists under hypoxic conditions, where hypoxia-inducible factor (HIF)-1α plays a critical role in maintaining its homeostasis. In osteoarthritis (OA), however, this hypoxic environment is disrupted, and decreased HIF-1α expression contributes to disease progression. HIF-prolyl hydroxylase (HIF-PH) inhibitors stabilize HIF-1α and are clinically used to treat renal anemia; therefore, they may also exert therapeutic effects in OA through the same mechanism. However, their effects on articular cartilage remain unclear. In this study, we investigated the effects of Roxadustat, a HIF-PH inhibitor, both in vitro using rat chondrocytes and in vivo using a monosodium iodoacetate (MIA)-induced rat OA model. Roxadustat showed no cytotoxicity and significantly increased the protein expression of HIF-1α, SRY-box transcription factor 9 (SOX9), and Aggrecan in monolayer cultures. In three-dimensional spheroid cultures, Roxadustat enhanced Safranin O staining and extracellular matrix production and significantly upregulated SOX9 and ACAN mRNA expression. Furthermore, intra-articular administration of Roxadustat in the MIA-induced OA model suppressed cartilage degeneration and significantly reduced the Modified Mankin score. These findings demonstrate that Roxadustat promotes anabolic responses in chondrocytes through stabilization of HIF-1α and suppresses cartilage degeneration in OA. Intra-articular administration of HIF-PH inhibitors may represent a novel disease-modifying therapeutic strategy for OA. Full article

(This article belongs to the Special Issue Molecular Biology of Hypoxia: 2nd Edition)

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