International Journal of Molecular Sciences

18 pages, 1517 KiB

Open AccessArticle

Renal and Vascular Effects of the Allosteric Transglutaminase 2 Modulator LDN-27219 in One-Kidney DOCA–Salt Mice

by Ian Mees, Judit Prat-Duran, Simon Comerma-Steffensen, Ulf Simonsen, Estéfano Pinilla and Niels Henrik Buus

Int. J. Mol. Sci. 2025, 26(12), 5724; https://doi.org/10.3390/ijms26125724 (registering DOI) - 14 Jun 2025

Abstract

The enzyme transglutaminase 2 (TG2) has an open conformation with transamidase activity which crosslinks matrix proteins contributing to fibrosis development. LDN-27219 promotes the closed conformation of TG2, which can enhance vasodilation, but its effects in renal tissue are unknown. We investigated whether LDN-27219 [...] Read more.

The enzyme transglutaminase 2 (TG2) has an open conformation with transamidase activity which crosslinks matrix proteins contributing to fibrosis development. LDN-27219 promotes the closed conformation of TG2, which can enhance vasodilation, but its effects in renal tissue are unknown. We investigated whether LDN-27219 treatment affects albuminuria and markers of renal fibrosis as well as ex vivo vasodilatation. Male C57BL/6 mice (n = 48) underwent unilateral nephrectomy plus insertion of a deoxycorticosterone acetate pellet (DOCA group) or nephrectomy only (sham group). Both groups were randomized to intraperitoneal treatment with either LDN-27219 (8 mg/kg twice daily) or vehicle for 2 weeks. Urine albumin excretion was evaluated by metabolic cages. Kidney tissue fibrosis markers were assessed by qPCR and Western blotting, while the TG2 conformational state was evaluated using native gel electrophoresis. Collagen staining was performed using Picrosirius red and quantified under circularly polarized light. Mesenteric arteries were mounted in wire myographs for evaluation of vasorelaxation. DOCA mouse developed significant albuminuria (p < 0.001 vs. sham), but neither TG2 mRNA nor protein expression was upregulated in the kidney. However, the relative amount of TG2 in the closed conformation was higher in DOCA mice. LDN-27219 did not affect albuminuria, but LDN-27219-treated DOCA mice showed less urine production and less collagen staining than vehicle-treated DOCA mice. LDN-27219 did not affect TG2 mRNA or TG2 protein expression or mRNA of fibrosis markers. LDN-27219-treated mice had enhanced vasorelaxation to the nitric oxide donor sodium nitroprusside. In conclusion, LDN-27219 treatment in the one-kidney DOCA–salt model did not affect renal TG2 mRNA and protein expression or albuminuria but still exerted beneficial effects in terms of reduced kidney fibrosis and urine production in addition to enhanced vasodilatation. Full article

(This article belongs to the Special Issue The Latest Molecular Research on Renal Disease)

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20 pages, 6642 KiB

Open AccessArticle

Lemon Verbena Extract Enhances Sleep Quality and Duration via Modulation of Adenosine A1 and GABA_A Receptors in Pentobarbital-Induced and Polysomnography-Based Sleep Models

by Mijoo Choi, Yean Kyoung Koo, Nayoung Kim, Yunjung Lee, Dong Joon Yim, SukJin Kim, Eunju Park and Soo-Jeung Park

Int. J. Mol. Sci. 2025, 26(12), 5723; https://doi.org/10.3390/ijms26125723 (registering DOI) - 14 Jun 2025

Abstract

This study investigated the effects of lemon verbena extract (LVE) on sleep regulation using both a pentobarbital-induced sleep model and an EEG-based sleep assessment model in mice. To elucidate its potential mechanisms, mice were randomly assigned to five groups: control, positive control (diazepam, [...] Read more.

This study investigated the effects of lemon verbena extract (LVE) on sleep regulation using both a pentobarbital-induced sleep model and an EEG-based sleep assessment model in mice. To elucidate its potential mechanisms, mice were randomly assigned to five groups: control, positive control (diazepam, 2 mg/kg b.w.), and three LVE-treated groups receiving 40, 80, or 160 mg/kg b.w. via oral administration. In the pentobarbital-induced sleep model, mice underwent a two-week oral administration of LVE, followed by intraperitoneal pentobarbital injections. The results demonstrated that LVE significantly shortened sleep latency and prolonged sleep duration compared to the control group. Notably, adenosine A1 receptor expression, both at the mRNA and protein levels, was markedly upregulated in the brains of LVE-treated mice. Furthermore, LVE’s administration led to a significant increase in the mRNA expression of gamma-aminobutyric acid type A (GABA_A) receptor subunits (α2 and β2) in brain tissue. In the electroencephalography (EEG)/electromyogram (EMG)-based sleep model, mice underwent surgical implantation of EEG and EMG electrodes, followed by one week of LVE administration. Quantitative EEG analysis revealed that LVE treatment reduced wakefulness while significantly enhancing REM and NREM sleep’s duration, indicating its potential sleep-promoting effects. These findings suggest that LVE may serve as a promising natural sleep aid, improving both the quality and duration of sleep through the modulation of adenosine and GABAergic signaling pathways. Full article

(This article belongs to the Special Issue Natural Medicines and Functional Foods for Human Health)

12 pages, 229 KiB

Open AccessReview

Acetyl Hexapeptide-8 in Cosmeceuticals—A Review of Skin Permeability and Efficacy

by Julita Zdrada-Nowak, Agnieszka Surgiel-Gemza and Magdalena Szatkowska

Int. J. Mol. Sci. 2025, 26(12), 5722; https://doi.org/10.3390/ijms26125722 (registering DOI) - 14 Jun 2025

Abstract

Biomimetic peptides represent a growing class of active ingredients in modern cosmeceuticals, designed to mimic the function of the naturally occurring peptides involved in skin homeostasis, repair, and regeneration. Among them, acetyl hexapeptide-8 (AH-8), often referred to as a “botox-like” peptide, has received [...] Read more.

Biomimetic peptides represent a growing class of active ingredients in modern cosmeceuticals, designed to mimic the function of the naturally occurring peptides involved in skin homeostasis, repair, and regeneration. Among them, acetyl hexapeptide-8 (AH-8), often referred to as a “botox-like” peptide, has received considerable attention for its potential to dynamically reduce wrinkles through the modulation of neuromuscular activity. AH-8 is widely used in topical formulations intended for anti-aging effects, scar treatment, and skin rejuvenation. This review provides a comprehensive overview of the structure and proposed mechanisms of action of AH-8, with particular focus on its efficacy and skin penetration properties. Due to its hydrophilic nature and relatively large molecular size, AH-8 faces limited permeability through the lipophilic stratum corneum, making effective dermal delivery challenging. Formulation strategies such as oil-in-water (O/W) and multiple water-in-oil-in-water (W/O/W) emulsions have been explored to enhance its delivery, but the ability of AH-8 to reach neuromuscular junctions remains uncertain. Preclinical and clinical studies indicate that AH-8 may reduce wrinkle depth, improve skin elasticity, and enhance hydration. However, the precise biological mechanisms underlying these effects—particularly the peptide’s ability to inhibit muscle contraction when applied topically—remain incompletely understood. In some studies, AH-8 has also shown beneficial effects in scar remodeling and sebum regulation. Despite promising cosmetic outcomes, AH-8’s low skin penetration limits its bioavailability and therapeutic potential. This review emphasizes the need for further research on formulation science and delivery systems, which are essential for optimizing the effectiveness of peptide-based cosmeceuticals and validating their use as non-invasive alternatives to injectable treatments. Full article

(This article belongs to the Special Issue Synthesis and Molecular Research of Drugs for Skin Diseases and Cosmetic Ingredients)

21 pages, 5292 KiB

Open AccessArticle

Downregulation of S6 Kinase and Hedgehog–Gli1 by Inhibition of Fatty Acid Synthase in AML with FLT3-ITD Mutation

by Maxim Kebenko, Ruimeng Zhuang, Konstantin Hoffer, Anna Worthmann, Stefan Horn, Malte Kriegs, Jan Vorwerk, Nikolas von Bubnoff, Cyrus Khandanpour, Niklas Gebauer, Sivahari Prasad Gorantla, Walter Fiedler, Carsten Bokemeyer and Manfred Jücker

Int. J. Mol. Sci. 2025, 26(12), 5721; https://doi.org/10.3390/ijms26125721 (registering DOI) - 14 Jun 2025

Abstract

Acute myeloid leukemia (AML) is a heterogeneous hematological malignancy associated with a poor prognosis. Activating mutations in the FLT3 gene occur in approximately 30% of AML cases, with internal tandem duplications in the juxtamembrane domain (FLT3-ITD; 75%) and mutations in the tyrosine kinase [...] Read more.

Acute myeloid leukemia (AML) is a heterogeneous hematological malignancy associated with a poor prognosis. Activating mutations in the FLT3 gene occur in approximately 30% of AML cases, with internal tandem duplications in the juxtamembrane domain (FLT3-ITD; 75%) and mutations in the tyrosine kinase domain (FLT3-TKD; 25%). FLT3-ITD mutations are linked to poor prognosis and offer significant clinical predictive value, whereas the implications of FLT3-TKD mutations are less understood. The Hedgehog–Gli pathway is an established therapeutic target in AML, and emerging evidence suggests crosstalk between FLT3-ITD signaling and Gli expression regulation via non-canonical mechanisms. Post-translational modifications involving myristic and palmitic acids regulate various cellular processes, but their role in AML remains poorly defined. In this study, we investigated the role of fatty acid synthase (FASN), which synthesizes myristic and palmitic acids and catalyzes palmitoyl-acyltransferation, in regulating FLT3-ITD-Gli signaling. FASN knockdown using shRNA and the FASN inhibitor TVB-3166 was performed in FLT3-ITD-mutated AML cell lines (MOLM13, MV411) and Baf3-FLT3-ITD cells. The impact of FASN inhibition was assessed through Western blot and kinome profiling, while biological implications were evaluated by measuring cell viability and proliferation. FASN inhibition resulted in reduced levels of phospho-Akt (pAkt) and phospho-S6 kinase (pS6) and decreased expression of Hedgehog–Gli1, confirming non-canonical regulation of Gli by FLT3-ITD signaling. Combining TVB-3166 with the Gli inhibitor GANT61 significantly reduced the survival of MOLM13 and MV411 cells. Full article

(This article belongs to the Special Issue Hematological Malignancies: Molecular Mechanisms and Therapy, 2nd Edition)

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21 pages, 2425 KiB

Open AccessArticle

HSD3B1 (c.1100C) Genotype Is Associated with Distinct Tumoral and Clinical Outcomes in Breast and Endometrial Cancers

by Nikitha Vobugari, Allison Makovec, Samuel Kellen, Shayan S. Nazari, Andrew Elliott, Devin Schmeck, Aiden Deacon, Gabriella von Dohlen, Emily John, Pedro C. Barata, Neeraj Agarwal, Melissa A. Geller, Britt K. Erickson, George Sledge, Julie H. Ostrander, Rana R. McKay, Charles J. Ryan, Nima Sharifi, Emmanuel S. Antonarakis and Justin Hwang

Int. J. Mol. Sci. 2025, 26(12), 5720; https://doi.org/10.3390/ijms26125720 (registering DOI) - 14 Jun 2025

Abstract

HSD3B1 encodes an enzyme that catalyzes the conversion of adrenal precursors into potent sex steroids. A common germline variant (c.1100C) enhances this effect and is linked to breast cancer (BC) progression. As the HSD3B1 genotypes contribute to differences in local and adrenal steroid [...] Read more.

HSD3B1 encodes an enzyme that catalyzes the conversion of adrenal precursors into potent sex steroids. A common germline variant (c.1100C) enhances this effect and is linked to breast cancer (BC) progression. As the HSD3B1 genotypes contribute to differences in local and adrenal steroid production, their transcriptional and phenotypic effects on cancers influenced by hormonal signaling such as BC and endometrial cancer (EC)—particularly in relation to menopausal status—remain unclear. We analyzed BC and EC sequenced from patients that received diagnostic tests in oncology clinics, and we determined the germline HSD3B1 c.1100 genotype (AA, AC, CC) from tumor DNA sequencing by using variant allele frequency, with inferred menopausal status assumed by age at molecular profiling. Whole-transcriptome RNA sequencing and gene set enrichment analysis showed that adrenal-permissive homozygous (CC) tumors in premenopausal ER + BC were enriched for hormone-related pathways, including Estrogen Response Early (NES ≈ +1.8). In premenopausal triple-negative BC, adrenal-restrictive homozygous (AA) tumors exhibited the elevated expression of immune and epithelial genes and the increased prevalence of MED12 alterations (AA 0.25% vs. CC 8%, p < 0.01). In endometrioid EC, CC tumors demonstrated the suppression of immune and proliferative pathways. Postmenopausal cases had higher progesterone receptor IHC positivity (AA 75% vs. CC 83%, p < 0.05) and numerically more frequent ESR1 copy number gains (AA 2.0% vs. CC 4.0%). Results highlight context-specific associations between germline HSD3B1 genotypes and tumor biology in BC and EC. Full article

(This article belongs to the Section Molecular Oncology)

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20 pages, 1377 KiB

Open AccessReview

The Multi-Dimensional Role of Vitamin D in the Pathophysiology and Treatment of Diabetic Foot Ulcers: From Molecular Mechanisms to Clinical Translation

by Weiwei Tang, Shengqiu Chen, Shuxia Zhang and Xingwu Ran

Int. J. Mol. Sci. 2025, 26(12), 5719; https://doi.org/10.3390/ijms26125719 (registering DOI) - 14 Jun 2025

Abstract

Diabetic foot ulcers (DFUs) constitute a severe and debilitating complication of diabetes, imposing a substantial global health burden due to their intricate pathophysiology and impaired wound healing processes. Vitamin D deficiency is highly prevalent among diabetic populations, and accumulating evidence indicates its potential [...] Read more.

Diabetic foot ulcers (DFUs) constitute a severe and debilitating complication of diabetes, imposing a substantial global health burden due to their intricate pathophysiology and impaired wound healing processes. Vitamin D deficiency is highly prevalent among diabetic populations, and accumulating evidence indicates its potential involvement in the pathogenesis and prognosis of DFUs. This review comprehensively explores the diverse roles of vitamin D in DFUs, encompassing its molecular mechanisms such as immunomodulation, promotion of angiogenesis, neuroprotection, and induction of antimicrobial peptides, as well as the metabolic characteristics associated with various vitamin D forms and compromised vitamin D receptor (VDR) signaling pathways. Although robust observational studies have established an association between vitamin D deficiency and adverse outcomes in DFUs, the clinical validation of supplementation efficacy through randomized controlled trials (RCTs) remains constrained by limitations such as small sample sizes, heterogeneity in study protocols, and insufficient long-term follow-up. This highlights the critical need for large-scale, high-quality studies to ascertain optimal treatment regimens and to cater to individualized patient requirements, particularly for individuals with obesity or those with renal impairments. Innovative strategies, such as the topical administration of vitamin D through intelligent delivery systems leveraging advanced biomaterials like nanofibers and hydrogels, exhibit substantial preclinical potential in enhancing stability, achieving targeted controlled release, and augmenting local biological effects, including the induction of antimicrobial peptides. Nevertheless, significant challenges persist in conclusively establishing clinical efficacy, comprehensively elucidating the underlying mechanisms, ensuring the safe translation of novel delivery systems, and developing personalized therapeutic strategies. The future success of these interventions hinges on meticulous research and interdisciplinary collaboration to seamlessly integrate validated vitamin D-based interventions into a comprehensive multidisciplinary management framework for DFUs, thereby holding promise for improving the clinical outcomes of this debilitating condition. Full article

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

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21 pages, 1218 KiB

Open AccessArticle

Comparison of Cognitive Deterioration Between Propofol and Remimazolam Anesthesia in ApoE4 Knock-In Mouse Model

by Jong-Ho Kim, Songyi Park, Harry Jung, Eun-Hae Lee, Eun-Seo Lee, Jae-Jun Lee and Jong-Hee Sohn

Int. J. Mol. Sci. 2025, 26(12), 5718; https://doi.org/10.3390/ijms26125718 (registering DOI) - 14 Jun 2025

Abstract

Perioperative neurocognitive disorder (PND) is a concern following anesthesia, particularly in individuals at risk for Alzheimer’s disease (AD). This study compared the cognitive and pathological effects of propofol and remimazolam in a mouse model with AD following surgery. Five-month-old male ApoE4-KI mice underwent [...] Read more.

Perioperative neurocognitive disorder (PND) is a concern following anesthesia, particularly in individuals at risk for Alzheimer’s disease (AD). This study compared the cognitive and pathological effects of propofol and remimazolam in a mouse model with AD following surgery. Five-month-old male ApoE4-KI mice underwent abdominal surgery under either propofol (170 mg/kg) or remimazolam (85 mg/kg) anesthesia. Cognitive function was assessed using the Morris water maze and Y-maze, and neuronal apoptosis and amyloid-beta (Aβ) deposition in the CA3 and dentate gyrus (DG) of the hippocampus were evaluated preoperatively and at 2, 4, and 7 days postoperatively. Both groups showed similar postoperative cognitive functions, with increased relative escape latency at day 2 and decreased relative spontaneous alternation at days 4 and 7. However, the neuropathological analysis revealed that propofol-induced significantly more neuronal death in the CA3 (days 4 and 7) and DG (days 2, 4, and 7), and greater Aβ accumulation in the CA3 (days 2 and 4) and DG (days 2 and 7) compared to remimazolam (p < 0.05). Propofol was associated with more pronounced neuropathologic changes in the hippocampus compared to remimazolam. These findings suggest remimazolam may be a safer anesthetic for patients at risk for neurodegenerative disorders, as it is associated with less severe hippocampal pathology, which is characteristic of AD. Full article

(This article belongs to the Section Molecular Neurobiology)

35 pages, 1675 KiB

Open AccessReview

Pathogenesis and Clinical Management of Metabolic Dysfunction-Associated Steatotic Liver Disease

by Roxana Liana Lucaciu, Sorina Cezara Coste, Adriana Corina Hangan, Mihaela Iancu, Olga Hilda Orășan, Angela Cozma, Sidonia Gog Bogdan and Lucia Maria Procopciuc

Int. J. Mol. Sci. 2025, 26(12), 5717; https://doi.org/10.3390/ijms26125717 (registering DOI) - 14 Jun 2025

Abstract

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic progressive liver disease with a substantial impact on global health. Given that MASLD has a complex etiology, it is a multisystemic disease, a multidisciplinary approach is required when treating MASLD. The optimal drug for [...] Read more.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a chronic progressive liver disease with a substantial impact on global health. Given that MASLD has a complex etiology, it is a multisystemic disease, a multidisciplinary approach is required when treating MASLD. The optimal drug for MASLD should diminish steatosis, fibrosis and inflammation in the liver. Although the pharmaceutical industry is still lagging in developing an approved pharmacologic therapy for MASLD, research has recently intensified, and many molecules that are in the final stages of clinical trials are expected to be approved in the coming few years. The current review updated information related to the MASLD pathogenesis, diagnosis and therapeutic options, how patients are clinically managed nowadays, and what to expect in the near future. Full article

(This article belongs to the Special Issue Metabolic Syndrome: New Insights in Pathogenesis, Diagnosis, Prevention, and Management)

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24 pages, 1368 KiB

Open AccessReview

Bacteria Under Metal Stress—Molecular Mechanisms of Metal Tolerance

by Ewa Oleńska, Wanda Małek, Izabela Swiecicka, Małgorzata Wójcik, Sofie Thijs and Jaco Vangronsveld

Int. J. Mol. Sci. 2025, 26(12), 5716; https://doi.org/10.3390/ijms26125716 (registering DOI) - 14 Jun 2025

Abstract

Metals are natural components of the lithosphere, whose amounts and bioavailability are increasing in many areas due to their continuous release from both natural sources and intensive human activities. Some metals are essential or beneficial for living organisms, while others are non-essential and [...] Read more.

Metals are natural components of the lithosphere, whose amounts and bioavailability are increasing in many areas due to their continuous release from both natural sources and intensive human activities. Some metals are essential or beneficial for living organisms, while others are non-essential and potentially toxic. When present at higher concentrations, even essential and beneficial metal ions can become harmful to all forms of life. Bacteria, unicellular organisms that have been exposed to metals since the earliest stages of life on Earth, have evolved metabolic pathways involving essential metals as well as diverse strategies to cope with metal toxicity. In the domain Bacteria, two main strategies have been identified: (i) metal exclusion, which includes cell wall sequestration and immobilization of metals in extracellular exopolysaccharides, siderophores, and other soluble microbial products, as well as (ii) metal tolerance, involving intracellular sequestration of metals (e.g., by metallothioneins, or low molecular weight thiols) as well as enzymatic conversion of metals to less toxic forms and/or its active efflux. Microorganisms possessing such adaptive traits are considered valuable agents for potential application in medicine, environmental sciences, and bioengineering (e.g., bioremediation and/or biomining). Full article

(This article belongs to the Section Molecular Microbiology)

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23 pages, 8837 KiB

Open AccessArticle

Supercritical Carbon Dioxide-Processed Acellular Dermal Matrix Patch for Enhanced Wound Healing

by Xinrui Zhang, Linh Thi Thuy Le, Yongxun Jin, Caijun Jin, Nguyen Ngan Giang, Thuy-Tien Thi Trinh, Yong Hyun Lee, Yong Woo Shin, Jin Woo Bae, Pham Ngoc Chien and Chan Yeong Heo

Int. J. Mol. Sci. 2025, 26(12), 5715; https://doi.org/10.3390/ijms26125715 (registering DOI) - 14 Jun 2025

Abstract

Wound healing remains a significant clinical challenge worldwide, and effective management strategies are essential for improving outcomes. This study evaluated SCderm Matrix, a novel acellular dermal matrix (ADM) patch developed using supercritical carbon dioxide (sCO₂) processing of human skin tissue. This [...] Read more.

Wound healing remains a significant clinical challenge worldwide, and effective management strategies are essential for improving outcomes. This study evaluated SCderm Matrix, a novel acellular dermal matrix (ADM) patch developed using supercritical carbon dioxide (sCO₂) processing of human skin tissue. This innovative processing method preserves structural integrity while enhancing biocompatibility, resulting in a patch characterized by porous architecture, uniform thickness, excellent tensile strength, and optical transparency. In vivo wound healing experiments using full-thickness skin wounds in Sprague–Dawley rats demonstrated the patch’s superior performance. Treatment with the sCO₂ ADM patch accelerated wound closure, reduced inflammation, and enhanced granulation tissue formation compared to both untreated controls and two commercially available ADM products. Histological analysis revealed improved re-epithelialization and collagen deposition, while molecular and immunohistochemical assessments showed decreased reactive oxygen species (ROS) and pro-inflammatory cytokines. Simultaneously, the treatment upregulated key proliferation and remodeling markers including alpha smooth muscle actin (α-SMA), vimentin, and transforming growth factor beta 1 (TGF-β1). These findings demonstrate that the SCderm Matrix promotes wound healing through multiple mechanisms: modulating inflammatory responses, enhancing antioxidant defenses, and supporting tissue regeneration. The results suggest this biomaterial has significant potential as an effective and versatile solution for clinical wound care applications. Full article

(This article belongs to the Special Issue Biomaterials for Wound Healing and Tissue Regeneration)

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19 pages, 2956 KiB

Open AccessArticle

Genomic Insights into Basal Diptera Phylogeny: The Non-Monophyletic Nature of Blephariceromorpha

by Yaoming Yang, Jiayao Ren, Xuhongyi Zheng, Lingna Cai, Jiayin Guan, Tianlong Cai, Xiaodong Xu and Ying Zhen

Int. J. Mol. Sci. 2025, 26(12), 5714; https://doi.org/10.3390/ijms26125714 (registering DOI) - 14 Jun 2025

Abstract

Diptera is one of the most ecologically significant and species-rich insect orders, but there are still unresolved phylogenetic relationships among its basal lineages, particularly within the infraorder Blephariceromorpha, due to limited molecular data. To address this gap, this study employs two parallel genomic [...] Read more.

Diptera is one of the most ecologically significant and species-rich insect orders, but there are still unresolved phylogenetic relationships among its basal lineages, particularly within the infraorder Blephariceromorpha, due to limited molecular data. To address this gap, this study employs two parallel genomic approaches: mitochondrial genomes and nuclear genomic analysis, covering 64 families and over 100 species of Diptera and their outgroups, to elucidate these phylogenetic relationships. Our results strongly support the monophyly of each constituent family (Blephariceridae, Deuterophlebiidae, and Nymphomyiidae), yet they reject the monophyly of Blephariceromorpha. Crucially, we found that Deuterophlebiidae and Nymphomyiidae form a sister group representing the basal-most lineage of Diptera, whereas Blephariceridae is positioned within Psychodomorpha. This indicates that the similar larval habitats and morphological traits shared between Blephariceridae and the Nymphomyiidae + Deuterophlebiidae clade are the result of convergent evolution. By resolving long-standing debates on the relationships within Blephariceromorpha and the basal lineages of Diptera, this study provides new insights into the evolutionary history of Diptera, especially within the suborder Nematocera. Full article

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

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16 pages, 599 KiB

Open AccessReview

Disease-Specific Novel Role of Growth Differentiation Factor 15 in Organ Fibrosis

by Harshal Sawant and Alip Borthakur

Int. J. Mol. Sci. 2025, 26(12), 5713; https://doi.org/10.3390/ijms26125713 (registering DOI) - 14 Jun 2025

Abstract

Growth Differentiation Factor 15 (GDF15), also known as non-steroidal anti-inflammatory drug-activated gene-1 (NAG-1) or macrophage inhibitory cytokine 1 (MIC-1), is a stress- and inflammation-induced cytokine distantly related to the TGF-β superfamily. Its highly elevated levels showed close association with various pathological conditions, making [...] Read more.

Growth Differentiation Factor 15 (GDF15), also known as non-steroidal anti-inflammatory drug-activated gene-1 (NAG-1) or macrophage inhibitory cytokine 1 (MIC-1), is a stress- and inflammation-induced cytokine distantly related to the TGF-β superfamily. Its highly elevated levels showed close association with various pathological conditions, making it an emerging biomarker of disease prognosis. However, most GDF15-mediated effects under normal physiology and various pathological conditions are poorly understood. This is partly because the only known GDF15 receptor is exclusively localized in the brain, and how GDF15 functions peripherally is currently unknown. Mounting recent evidence has shown GDF15’s critical role in fibrosis in multiple organs, such as the liver, lung, and kidney. Evidence further suggests that it can either contribute to fibrosis by promoting inflammation and fibroblast activation or confer protective effects by modulating the immune response and mitigating fibrosis severity. Thus, the exact role of GDF15 in fibrosis can vary depending on the organ involved and the specific disease context. For example, increased GDF15 in idiopathic pulmonary fibrosis (IPF) promotes fibrosis via fibroblast activation and collagen deposition. Conversely, GDF15 might have a protective role in liver fibrosis, with decreased GDF15 levels causing increased fibrosis severity, while GDF15 treatment ameliorates fibrosis. Due to its close association with fibrosis, GDF15 is being investigated as a potential biomarker for disease severity and monitoring treatment response. However, further research unraveling its mechanisms of action is needed to explore the potential of GDF15 as a therapeutic target for treating fibrosis, either by modulating its expression or utilizing its immunomodulatory properties. This review marshals the limited studies addressing the recently appreciated differential role of GDF15 in regulating the fibrotic process in different organs. The review also discusses the aspects of further research needed to highlight GDF 15 as a novel predictor and therapeutic target for fibrosis in different organs. Full article

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

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18 pages, 1684 KiB

Open AccessArticle

Harnessing Light Wavelengths to Enrich Health-Promoting Molecules in Tomato Fruits

by Bruno Hay Mele, Ermenegilda Vitale, Violeta Velikova, Tsonko Tsonev, Carolina Fontanarosa, Michele Spinelli, Angela Amoresano and Carmen Arena

Int. J. Mol. Sci. 2025, 26(12), 5712; https://doi.org/10.3390/ijms26125712 (registering DOI) - 14 Jun 2025

Abstract

The tomato (Solanum lycopersicum L.) is one of the most consumed crops worldwide and a source of antioxidants. Given the role the latter play against oxidative stress and free radical-related diseases, enhancing tomato bioactive compound production would be appealing for a wide [...] Read more.

The tomato (Solanum lycopersicum L.) is one of the most consumed crops worldwide and a source of antioxidants. Given the role the latter play against oxidative stress and free radical-related diseases, enhancing tomato bioactive compound production would be appealing for a wide range of applications in the fields of nutrition, pharmacy, and biotechnology. This study explores a sustainable and innovative approach: the modulation of specific light spectra to boost the production of bioactive compounds in tomatoes (cultivar ‘Microtom’). We investigated how three light regimes—white fluorescent (FL), full-spectrum (FS), and red-blue (RB)—influence the accumulation of polyphenols and other key nutraceuticals during plant growth. Our findings reveal that full-spectrum (FS) light significantly enhances the levels of polyphenols, flavonoids, tannins, ascorbic acid, and lycopene in tomato fruits, compared to those grown under RB or FL light. Interestingly, fruits from RB light-grown plants showed the highest carotenoid concentrations and antioxidant capacity. These results suggest that light quality actively modulates the expression of key enzymes in the phenylpropanoid and flavonoid biosynthetic pathways, shaping each fruit’s unique metabolic fingerprint. Cluster analysis confirmed that RB, FL, and FS conditions lead to distinct polyphenolic profiles, each with notable health-promoting potential. Our results highlight a promising avenue: tailoring light environments to enhance the functional value of crops, bridging agriculture, nutrition, and biomedicine in a sustainable way. Full article

(This article belongs to the Special Issue Health-Promoting Effects of Medicinal and Edible Plants and Their Molecular Mechanism)

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21 pages, 2396 KiB

Open AccessReview

Co-Culture Approaches in Cartilage and Bone Tissue Regeneration

by Iwona Deszcz and Julia Bar

Int. J. Mol. Sci. 2025, 26(12), 5711; https://doi.org/10.3390/ijms26125711 (registering DOI) - 14 Jun 2025

Abstract

Cartilage and bone defects as well as osteoarthritis are prevalent worldwide, affecting individuals across all age groups, from young, active populations to older adults. The standard protocol in cartilage regeneration involves knee replacement surgery through the implantation of an endoprosthesis. Current clinical protocols [...] Read more.

Cartilage and bone defects as well as osteoarthritis are prevalent worldwide, affecting individuals across all age groups, from young, active populations to older adults. The standard protocol in cartilage regeneration involves knee replacement surgery through the implantation of an endoprosthesis. Current clinical protocols involving cell-based therapies are associated with limitations, including the lack of functional cartilage-like tissue and dedifferentiation of chondrocyte, particularly during monoculture. Similarly, in bone regeneration, the “gold standard” is the use of bone auto- or allografts, which are associated with immunological rejection, inadequate vascularization, and limited osteogenesis. To overcome these limitations, various co-culture techniques have been introduced as promising strategies for cartilage and bone tissue regeneration. These systems aim to mimic native microenvironments by promoting interactions between chondrocytes and mesenchymal stromal cells (MSCs) in cartilage repair and between osteogenic and angiogenic cells in bone regeneration. This paper introduces different co-culture systems focusing on in vitro crosstalk between MSCs derived from various sources and other somatic cell populations in cartilage and bone regeneration. Full article

(This article belongs to the Special Issue Recent Advances in Adult Stem Cell Research)

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16 pages, 2250 KiB

Open AccessArticle

Oxamate, an LDHA Inhibitor, Inhibits Stemness, Including EMT and High DNA Repair Ability, Induces Senescence, and Exhibits Radiosensitizing Effects in Glioblastoma Cells

by Takuma Hashimoto, Go Ushikubo, Naoya Arao, Khaled Hatabi, Kazuki Tsubota and Yoshio Hosoi

Int. J. Mol. Sci. 2025, 26(12), 5710; https://doi.org/10.3390/ijms26125710 (registering DOI) - 14 Jun 2025

Abstract

Enhancement of glycolysis has been reported in tumor cells, and it is believed that this enhancement is important for maintaining the stemness of tumor cells and contributes to malignant phenotypes. Here, we investigated the effects of Oxamate, which inhibits glycolysis by blocking the [...] Read more.

Enhancement of glycolysis has been reported in tumor cells, and it is believed that this enhancement is important for maintaining the stemness of tumor cells and contributes to malignant phenotypes. Here, we investigated the effects of Oxamate, which inhibits glycolysis by blocking the conversion of pyruvate to lactate, on radiosensitivity and its molecular mechanisms in T98G glioblastoma cells. Oxamate significantly enhanced radiosensitivity by delaying DNA repair, as indicated by the persistence of γ-H2AX foci up to four days post-irradiation. Mechanistically, Oxamate suppressed the expression and phosphorylation of key DNA repair factors. Furthermore, Oxamate induced apoptosis and promoted cellular senescence, as evidenced by the accumulation of SA-β-gal and the upregulation of pS15-p53 and p21. In addition, Oxamate downregulated EGFR expression, reduced the levels of stem cell markers, and modulated epithelial–mesenchymal transition (EMT) markers, suggesting a potential suppression of EMT-related pathways. Together, these results demonstrate that Oxamate enhances radiosensitivity in glioblastoma cells through multiple mechanisms, including the inhibition of DNA repair, induction of apoptosis and senescence, and suppression of cancer stem cell properties and EMT. Our findings provide new insights into the potential use of Oxamate as a radiosensitizer and warrant further investigation of its clinical application in glioblastoma therapy. Full article

(This article belongs to the Special Issue Current Developments in Glioblastoma Research and Therapy: 2nd Edition)

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19 pages, 2634 KiB

Open AccessArticle

From Gene to Pathways: Understanding Novel Vps51 Variant and Its Cellular Consequences

by Damla Aygun and Didem Yücel Yılmaz

Int. J. Mol. Sci. 2025, 26(12), 5709; https://doi.org/10.3390/ijms26125709 (registering DOI) - 14 Jun 2025

Abstract

Disorders of vesicular trafficking and genetic defects in autophagy play a critical role in the development of metabolic and neurometabolic diseases. These processes govern intracellular transport and lysosomal degradation, thereby maintaining cellular homeostasis. In this article, we present two siblings with a novel [...] Read more.

Disorders of vesicular trafficking and genetic defects in autophagy play a critical role in the development of metabolic and neurometabolic diseases. These processes govern intracellular transport and lysosomal degradation, thereby maintaining cellular homeostasis. In this article, we present two siblings with a novel homozygous variant in VPS51 (Vacuolar protein sorting 51) gene (c.1511C>T; p.Thr504Met), exhibiting developmental delay, a thin corpus callosum, severe intellectual disability, epilepsy, microcephaly, hearing loss, and dysphagia. This study aimed to investigate the effects of the novel VPS51 gene variation at the RNA and protein level in fibroblasts derived from patients. A comparative proteomic analysis, which has not been previously elucidated, was performed to identify uncharacterized proteins associated with vesicular trafficking. Furthermore, the impact of disrupted pathways on mitochondria–lysosome contact sites was assessed, offering a thorough pathophysiological evaluation of GARP/EARP (Golgi Associated Retrograde Protein / Endosome Associated Retrograde Protein) complex dysfunction. An analysis of mRNA expression indicated decreased levels of the VPS51 gene, alongside modifications in the expression of autophagy-related genes (LC3B, p62, RAB7A, TBC1D15). Western blotting demonstrated a reduction in VPS51 and autophagy-related protein levels. Proteomic profiling revealed 585 differentially expressed proteins, indicating disruptions in vesicular trafficking, lysosomal function, and mitochondrial metabolism. Proteins involved in mitochondrial β-oxidation and oxidative phosphorylation exhibited downregulation, whereas pathways related to glycolysis and lipid synthesis showed upregulation. Live-cell confocal microscopy revealed a notable increase in mitochondria–lysosome contact sites in patient fibroblasts, suggesting that VPS51 protein dysfunction contributes to impaired organelle communication. The findings indicate that the novel VPS51 gene variation influences intracellular transport, autophagy, and metabolic pathways, offering new insights into its involvement in neurometabolic disorders. Full article

(This article belongs to the Special Issue Genomic Research of Rare Diseases)

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8 pages, 854 KiB

Open AccessCommunication

Onvansertib-Based Second-Line Therapies in Combination with Gemcitabine and Carboplatin in Patient-Derived Platinum-Resistant Ovarian Carcinomas

by Federica Guffanti, Ilaria Mengoli, Francesca Ricci, Ludovica Perotti, Elena Capellini, Laura Sala, Simone Canesi, Chu-Chiao Wu, Robert Fruscio, Maya Ridinger, Giovanna Damia and Michela Chiappa

Int. J. Mol. Sci. 2025, 26(12), 5708; https://doi.org/10.3390/ijms26125708 (registering DOI) - 14 Jun 2025

Abstract

Platinum resistance represents an urgent medical need in the management of ovarian cancer. The activity of the combinations of onvansertib, an inhibitor of polo-like kinase 1, with gemcitabine or carboplatin was tested using patient-derived xenografts of high-grade serous ovarian carcinoma resistant to cisplatin [...] Read more.

Platinum resistance represents an urgent medical need in the management of ovarian cancer. The activity of the combinations of onvansertib, an inhibitor of polo-like kinase 1, with gemcitabine or carboplatin was tested using patient-derived xenografts of high-grade serous ovarian carcinoma resistant to cisplatin (DDP). Two PDX models were selected from our xenobank: one with acquired resistance to DDP (#266R) and the other (#315) with intrinsic DDP resistance. Tumor-bearing mice were randomized to receive vehicle, single onvansertib, gemcitabine and carboplatin, and their combinations. Onvansertib/gemcitabine and onvansertib/carboplatin combinations were well tolerated. In the #266R model, single drug treatments were completely inactive, while the combinations of onvansertib/gemcitabine and onvansertib/carboplatin resulted in a significant increase in survival compared to controls and single drugs (p < 0.001 versus control, onvansertib, gemcitabine and carboplatin). Similar efficacy was observed in the s.c. #315 PDX model; indeed, onvansertib and carboplatin monotherapies were inactive, gemcitabine monotherapy was marginally active, while both combinations were highly active. The molecular mechanism underlying the efficacy of the combinations suggests a higher induction of DNA damage which seems plausible considering that, in both cases, gemcitabine and carboplatin, respectively, interfere with DNA metabolism and induce alkylation damage. The results suggest that the combinations of onvansertib/gemcitabine and onvansertib/carboplatin are safe and were shown to be of therapeutic value in the platinum-resistant setting of ovarian carcinoma, strongly supporting their clinical translatability. Full article

(This article belongs to the Special Issue Resistance to Therapy in Ovarian Cancers)

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17 pages, 880 KiB

Open AccessArticle

Endocannabinoid Tone and Oxylipins in Rheumatoid Arthritis and Osteoarthritis—A Novel Target for the Treatment of Pain and Inflammation?

by Jost Klawitter, Andrew D. Clauw, Jennifer A. Seifert, Jelena Klawitter, Bridget Tompson, Cristina Sempio, Susan L. Ingram, Uwe Christians and Larry W. Moreland

Int. J. Mol. Sci. 2025, 26(12), 5707; https://doi.org/10.3390/ijms26125707 (registering DOI) - 14 Jun 2025

Abstract

Inflammation is a complicated physiological process that contributes to a variety of disorders including osteoarthritis (OA) and rheumatoid arthritis (RA). Endocannabinoids and the endocannabinoid system (ECS) play a pivotal role in the physiological response to pain and inflammation. A clinical study to investigate [...] Read more.

Inflammation is a complicated physiological process that contributes to a variety of disorders including osteoarthritis (OA) and rheumatoid arthritis (RA). Endocannabinoids and the endocannabinoid system (ECS) play a pivotal role in the physiological response to pain and inflammation. A clinical study to investigate the role of the endocannabinoid system and related lipids in pain and inflammation in OA and RA was performed. In total, 80 subjects, namely, 25 patients with RA, 18 with OA, and 37 healthy participants, were included. Sixteen endocannabinoids and congeners, as well as 129 oxylipins, were quantified in plasma using specific, quantitative LC-MS/MS assays. The endocannabinoid analysis revealed significantly lower levels of 2-arachidonoylglycerol (2-AG) in RA and OA patients compared to healthy participants. In contrast, the EC levels of the ethanolamide group (anandamide, docosahexaenoyl-EA, palmitoleoyl-EA, and other ethanolamides) were higher in the RA study cohort and to a lesser extent also in the OA cohort. This analysis of oxylipins revealed lower levels of the pro-resolving lipid 9-oxo-octadecadienoic acid (9-oxoODE) and the ω-3 fatty acids EPA (eicosapentaenoic acid) and DHA (docosahexaenoic acid) in RA compared to all other study cohorts. 2-AG is a key regulator of nociception and inflammation, and its relatively low levels might be a mechanistic contributor to residual pain and inflammation in RA and OA. Several changes in pro- and anti-inflammatory lipid mediators were detected, including lower levels of EPA and DHA in RA, which might reveal the potential for nutritional supplementation with these anti-inflammatory fatty acids. Full article

(This article belongs to the Special Issue Rheumatoid Arthritis: Molecular Mechanisms and Immunotherapy)

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12 pages, 1268 KiB

Open AccessArticle

The Effects of Lutein-Containing Supplement Intake on Glycation Inhibition Among Diabetic Patients with Cataracts

by Rijo Hayashi, Shimmin Hayashi and Shigeki Machida

Int. J. Mol. Sci. 2025, 26(12), 5706; https://doi.org/10.3390/ijms26125706 (registering DOI) - 13 Jun 2025

Abstract

Glycation is known as an important factor inducing human diseases, including diabetic complications. As oxidative stress contributes to procedures of glycation, antioxidants may inhibit glycation and delay the progression of diabetic complications. Our previous investigation of human aqueous humor after the intake of [...] Read more.

Glycation is known as an important factor inducing human diseases, including diabetic complications. As oxidative stress contributes to procedures of glycation, antioxidants may inhibit glycation and delay the progression of diabetic complications. Our previous investigation of human aqueous humor after the intake of a lutein-containing supplement demonstrated increases in antioxidative activities and decreases in peroxidative products. This study enrolled 25 patients with diabetes (DM group) and 100 age-matched controls. Aqueous humor samples were collected during cataract surgery before and after 6 weeks of oral intake of the lutein-containing antioxidant supplement, Ocuvite + Lutein^®. The carboxymethyl-lysine level (CML) was measured as an indicator of glycation. Levels of superoxide dismutase activities (SOD) and total hydroperoxide (TH) were measured as indicators of oxidation. Changes after intake and the differences between age-matched controls and the DM group were evaluated. CML decreased after intake among the DM group, while there were no changes among the age-matched controls. SOD was significantly lower and TH was significantly higher in the DM group as compared to the age-matched controls, both before and after intake. In line with the decreases in glycation, the intake of lutein-containing antioxidant supplements may inhibit diabetic complications in diabetic patients. Full article

(This article belongs to the Special Issue The Role of Oxidative Stress and Antioxidants in Human Disease)

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11 pages, 1101 KiB

Open AccessCommunication

Imaging the Binding Between Dasatinib and Its Target Protein in Living Cells Using an SLP Tag System on Intracellular Compartments

by Da Kyeong Park, Sang-Hee Lee, Hee-Seok Kweon, Zee-Won Lee and Kyung-Bok Lee

Int. J. Mol. Sci. 2025, 26(12), 5705; https://doi.org/10.3390/ijms26125705 (registering DOI) - 13 Jun 2025

Abstract

Interactions between chemical drugs and their target proteins are fundamental to drug screening and precision therapy in modern clinical medicine. However, elucidating these interactions within living cells remains challenging due to the limited availability of efficient detection methods. Despite substantial efforts, technical limitations [...] Read more.

Interactions between chemical drugs and their target proteins are fundamental to drug screening and precision therapy in modern clinical medicine. However, elucidating these interactions within living cells remains challenging due to the limited availability of efficient detection methods. Despite substantial efforts, technical limitations still impede the identification of direct interactors. In this study, we present a simple method to detect the binding between a chemical drug and its target proteins in live cells. This approach utilizes a self-labeling protein (SLP) tag system, specifically HaloTag which is a modified haloalkane dehalogenase, combined with spatially localized expression of the SLP. To implement this system, dasatinib was conjugated to a HaloTag ligand, and the HaloTag protein was expressed in specific intracellular compartments, such as endosomes or F-actin structures. Upon treatment of cells with the HaloTag ligand-conjugated dasatinib, green fluorescent protein (GFP)-fused cytoplasmic dasatinib target proteins were observed to co-localize with the HaloTag at these subcellular structures, thereby indicating direct drug–target binding. This method provides a good spatial resolution with a high signal-to-noise ratio and low false-positive signals across a high background and false-positive/false-negative signals from endogenous proteins and/or non-specific binding. In this context, we believe that our method is a useful platform for visualizing the binding between chemical drugs and their cytoplasmic targets within living systems. Full article

(This article belongs to the Section Biochemistry)

11 pages, 2716 KiB

Open AccessCommunication

Whole-Exome Sequencing Analysis of Inflammatory Bowel Disease-Associated Serrated Dysplasia

by Zsófia Balajthy, Szintia Almási, Tamás Lantos, Levente Kuthi, Georgios Deftereos, Won-Tak Choi and Anita Sejben

Int. J. Mol. Sci. 2025, 26(12), 5704; https://doi.org/10.3390/ijms26125704 (registering DOI) - 13 Jun 2025

Abstract

The clinicopathologic and molecular features of serrated lesions with dysplasia in inflammatory bowel disease (IBD) remain poorly understood. We examined a total of 2396 patients treated for IBD at the University of Szeged between 2011 and 2023. Among them, 177 (7%) patients were [...] Read more.

The clinicopathologic and molecular features of serrated lesions with dysplasia in inflammatory bowel disease (IBD) remain poorly understood. We examined a total of 2396 patients treated for IBD at the University of Szeged between 2011 and 2023. Among them, 177 (7%) patients were diagnosed with colorectal neoplasia, of which only 11 (6%) had serrated dysplasia (n = 13). Of the 13 lesions, 5 (38%) showed features of sessile serrated lesion (SSL)-like dysplasia; 1 (8%) exhibited characteristics of traditional serrated adenoma (TSA)-like dysplasia; 6 (46%) were classified as serrated dysplasia, not otherwise specified (NOS); and 1 (8%) displayed mixed features of SSL-like and TSA-like dysplasias. At the time of the serrated dysplasia diagnosis, the mean age of the patients was 56 years. Ten (91%) patients had ulcerative colitis, and one (9%) had Crohn’s disease. Pancolitis was observed in seven (64%) patients. The mean duration of IBD at the time of the serrated dysplasia diagnosis was 26 years. Most lesions (n = 9; 69%) were found in the left colon, including SSL-like dysplasia (3/5; 60%) and serrated dysplasia NOS (5/6, 83%). Eleven (85%) lesions had a polypoid endoscopic appearance. The mean size of the serrated dysplasia was 0.8 cm. Most lesions (n = 8; 62%) showed low-grade dysplasia. Serrated dysplasia was often associated with conventional (n = 3; 27%) or nonconventional dysplasia (n = 3; 27%). During the follow-up, 5 (45%) of the 11 patients developed colorectal cancer, including 3 patients with serrated dysplasia NOS, 1 with SSL-like dysplasia, and 1 with TSA-like dysplasia. Whole-exome sequencing revealed that the SSL-like dysplasia harbored mutations in BRAF (p.V600E), MLH1, KRAS, PTEN, POLE, KMT2C, and/or EXT1, whereas the serrated dysplasia NOS showed mutations in TP53, POLG, BRAF (p.G469A), KMT2C, and/or EXT1. One patient with both SSL-like dysplasia and mixed SSL-like/TSA-like dysplasia carried a pathogenic MUTYH (p.R217H) mutation, along with mutations in MADD. Serrated dysplasia was rare in IBD, with a prevalence rate of 6%. The SSL-like dysplasia exhibited distinct clinicopathologic and molecular characteristics compared with its sporadic counterpart. Similarly, serrated dysplasia NOS displayed unique molecular features compared with SSL-like dysplasia and could carry a higher risk of malignancy. Full article

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

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28 pages, 733 KiB

Open AccessReview

Comparative Analysis of Melatonin and Polydeoxyribonucleotide: Possible Benefits of Co-Treatment Effects and Potential Synergistic Applicability

by Su Kil Jang, Jaeseok Choi, Hye Won Lim, Hong-Gyum Kim and Yeong-Min Yoo

Int. J. Mol. Sci. 2025, 26(12), 5703; https://doi.org/10.3390/ijms26125703 (registering DOI) - 13 Jun 2025

Abstract

This paper explores the enhancement of pharmacological outcomes through the combined use of melatonin and polydeoxyribonucleotide (PDRN), hypothesizing that their simultaneous application might surpass the effectiveness of individual use. Melatonin is a hormone that modulates sleep, oxidative stress and inflammation, and exerts analgesic [...] Read more.

This paper explores the enhancement of pharmacological outcomes through the combined use of melatonin and polydeoxyribonucleotide (PDRN), hypothesizing that their simultaneous application might surpass the effectiveness of individual use. Melatonin is a hormone that modulates sleep, oxidative stress and inflammation, and exerts analgesic and anti-inflammatory effects. Conversely, PDRN is well-known for its significant contributions to tissue regeneration and its role in promoting angiogenesis. This article details the pharmacological effects and mechanisms of each compound, suggesting that their integration could amplify their individual benefits, particularly in the realms of wound healing and various medical applications. This paper seeks to provide a comprehensive analysis of the interactions between melatonin and PDRN by reviewing existing studies, thereby paving the way for novel therapeutic strategies. It emphasizes the need for further clinical trials and research to optimize the use of this combination for the improved treatment of diverse cellular or tissue conditions. In conclusion, further research is needed to optimize combination therapies involving melatonin and PDRN, with the goal of confirming their enhanced benefits when used together. In conclusion, further research is necessary to optimize combination therapies involving melatonin and PDRN to confirm their enhanced benefits when used in conjunction. This review emphasizes the importance of exploring their potential synergistic effects and developing effective therapeutic strategies across various medical disciplines. Full article

(This article belongs to the Special Issue A Moving Frontline in the Study of Melatonin and Its Analogs)

18 pages, 3941 KiB

Open AccessArticle

Characterization and Expression Analysis of the PvTLP Gene Family in the Common Bean (Phaseolus vulgaris) in Response to Salt and Drought Stresses

by Xue Dong, Min Zhao, Jia Li, Fuyi Qiu, Yan Wang, Jiandong Zhao, Jianwu Chang and Xiaopeng Hao

Int. J. Mol. Sci. 2025, 26(12), 5702; https://doi.org/10.3390/ijms26125702 (registering DOI) - 13 Jun 2025

Abstract

Tubby-like proteins (TLPs) are essential multifunctional transcription factors in plants that significantly influence plant growth and development, signal transduction, and adaptation to environmental stress. Despite their importance, there is limited knowledge of the identification and functional roles of the TLP gene family in [...] Read more.

Tubby-like proteins (TLPs) are essential multifunctional transcription factors in plants that significantly influence plant growth and development, signal transduction, and adaptation to environmental stress. Despite their importance, there is limited knowledge of the identification and functional roles of the TLP gene family in the common bean. In this study, we identified the PvTLP gene family, which consists of 10 PvTLP genes distributed unevenly across seven chromosomes. Phylogenetic analysis revealed that these genes could be classified into three subfamilies (A, B, and C). All PvTLP proteins contained both conserved tubby and F-box domains, with the exception of PvTLP7, which lacks the F-box domain. Conserved motif analysis revealed that 10 PvTLP genes contained motif 1 and motif 3. Cis-acting elements analysis indicated that PvTLP genes might be involved in light, hormone, and stress responses. Synteny analysis revealed a closer phylogenetic relationship between the common bean and dicotyledons than monocotyledons. qRT-PCR analysis confirmed the significant differences in the expression of most PvTLP genes in both leaves and roots under salt and drought stresses. These findings provide valuable insights for further exploration of the molecular functions of TLPs in plant responses to various stresses and offer key candidate genes for enhancing stress resistance in the common bean through molecular breeding. Full article

(This article belongs to the Special Issue Research on Plant Genomics and Breeding: 2nd Edition)

24 pages, 2180 KiB

Open AccessReview

Targeting WEE1 Kinase for Breast Cancer Therapeutics: An Update

by Zhao Zhang, Ritika Harish, Naveed Elahi, Sawanjit Saini, Aamir Telia, Manjit Kundlas, Allexes Koroleva, Israel N. Umoh, Manpreet Lota, Meha Bilkhu, Aladdin Kawaiah, Manogna R. Allala, Armelle Leukeu, Emmanuel Nebuwa, Nadiya Sharifi, Anthony W. Ashton, Xuanmao Jiao and Richard G. Pestell

Int. J. Mol. Sci. 2025, 26(12), 5701; https://doi.org/10.3390/ijms26125701 (registering DOI) - 13 Jun 2025

Abstract

WEE1 kinase is a crucial cell cycle regulatory protein that controls the timing of mitotic entry. WEE1, via inhibition of Cyclin-dependent Kinase 1 (CDK1) and Cyclin-dependent Kinase 2 (CDK2), governs the G2-M checkpoint by inhibiting entry into mitosis. The state of balance between [...] Read more.

WEE1 kinase is a crucial cell cycle regulatory protein that controls the timing of mitotic entry. WEE1, via inhibition of Cyclin-dependent Kinase 1 (CDK1) and Cyclin-dependent Kinase 2 (CDK2), governs the G2-M checkpoint by inhibiting entry into mitosis. The state of balance between WEE family kinases and CDC25C phosphatases restricts CDK1/CycB activity. The WEE kinase family consists of WEE1, PKMYT1, and WEE2 (WEE1B). WEE1 and PKMYT1 regulate entry into mitosis during cell cycle progression, whereas WEE2 governs cell cycle progression during meiosis. Recent studies have identified WEE1 as a potential therapeutic target in several cancers, including therapy-resistant triple-negative breast cancer. Adavosertib’s clinical promise was challenged by inter-individual variations in response and side effects. Because of these promising preclinical outcomes, other WEE1 kinase inhibitors (Azenosertib, SC0191, IMP7068, PD0407824, PD0166285, WEE1-IN-5, Zedoresertib, WEE1-IN-8, and ATRN-1051) are being developed, with several currently being evaluated in clinical trials or as an adjuvant to chemotherapies. Preclinical studies show WEE1 inhibitors induce MHC class 1 antigens and STING when given as combination therapies, suggesting potential additional therapeutic opportunities. Reliable predictors of clinical responses based on mechanistic insights remain an important unmet need. Herein, we review the role of WEE1 inhibition therapy in breast cancer. Full article

(This article belongs to the Special Issue Molecular Research and Treatment of Breast Cancer: 3rd Edition)

13 pages, 1385 KiB

Open AccessArticle

HPTAS: An Alignment-Free Haplotype Phasing Algorithm Focused on Allele-Specific Studies Using Transcriptome Data

by Jianan Wang, Zhenyuan Sun, Guohua Wang and Yan Miao

Int. J. Mol. Sci. 2025, 26(12), 5700; https://doi.org/10.3390/ijms26125700 (registering DOI) - 13 Jun 2025

Abstract

Haplotype phasing refers to determining the haplotype sequences inherited from each parent in a diploid organism. It is a critical process for various downstream analyses, and numerous haplotype phasing methods for genomic single nucleotide polymorphisms (SNPs) have been developed. Allele-specific (AS) expression and [...] Read more.

Haplotype phasing refers to determining the haplotype sequences inherited from each parent in a diploid organism. It is a critical process for various downstream analyses, and numerous haplotype phasing methods for genomic single nucleotide polymorphisms (SNPs) have been developed. Allele-specific (AS) expression and alternative splicing play key roles in diverse biological processes. AS studies usually focus more on exonic SNPs, and multiple phased SNPs need to be combined to obtain better inferences. In this paper, we introduce an alignment-free algorithm HPTAS for haplotype phasing in AS studies. Instead of using sequence alignment to count the number of reads covering SNPs, HPTAS constructs a mapping structure from transcriptome annotations and SNPs and employs a k-mer-based approach to derive phasing counts from RNA-seq data. Using both next-generation sequencing (NGS) and the third-generation sequencing (TGS) NA12878 RNA-seq data and comparing with the most advanced algorithm in the field, we have demonstrated that HPTAS achieves high phasing accuracy and performance and that transcriptome data indeed facilitates the phasing of exonic SNPs. With the continued advancement of sequencing technology and the improvement in transcriptome annotations, HPTAS may serve as a foundation for future haplotype phasing methods. Full article

(This article belongs to the Special Issue New Computational Methodologies for Biomolecule Sequence, Structure and Function Discovery)

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18 pages, 771 KiB

Open AccessArticle

Metabolic and Inflammatory Biomarkers Predicting Sarcopenic Obesity and Cardiometabolic Risk in Arab Women: A Cross-Sectional Study

by Gregory Livshits, Nader Tarabeih, Alexander Kalinkovich, Adel Shalata and Shai Ashkenazi

Int. J. Mol. Sci. 2025, 26(12), 5699; https://doi.org/10.3390/ijms26125699 (registering DOI) - 13 Jun 2025

Abstract

The sarcopenic obesity-related phenotype (SOP) is defined by the coexistence of sarcopenia and obesity, leading to heightened disability, morbidity, and mortality. Its multifactorial pathogenesis involves chronic inflammation and metabolic alterations. In this cross-sectional study, 562 women were classified into four groups: control, sarcopenic, [...] Read more.

The sarcopenic obesity-related phenotype (SOP) is defined by the coexistence of sarcopenia and obesity, leading to heightened disability, morbidity, and mortality. Its multifactorial pathogenesis involves chronic inflammation and metabolic alterations. In this cross-sectional study, 562 women were classified into four groups: control, sarcopenic, obese, and SOP. Body composition measurements, including fat mass, skeletal muscle mass, and extracellular water (ECW), were assessed using the bioimpedance method. Several inflammatory biomarkers were measured in plasma samples by ELISA. Discriminant function analysis identified age, ECW, chemerin, the systemic immune-inflammation index (SII), and the ratio of total cholesterol to high-density lipoprotein cholesterol (TC/HDL-C) as significant discriminators among groups, clearly distinguishing SOP from control. Multivariable logistic regression analysis revealed that these variables were independently associated with SOP status (SOP vs. control), regardless of age, with odds ratios (ORs) ranging from 1.87 (95% confidence interval [CI]: 1.23–2.85) for SII to 7.77 (95% CI: 3.67–16.44) for ECW. A generalized estimating equation (GEE) analysis further demonstrated that SOP significantly increased the odds (OR: 3.04; 95% CI: 1.39–6.67) of multimorbidity (hypertension (HTN) + hyperlipidemia (HLD) + type 2 diabetes (D2T)). These findings suggest SOP is a clinically relevant phenotype linked to cardiometabolic comorbidities and systemic inflammation. Identifying SOP using accessible body composition and biomarker assessments may support early risk stratification and guide personalized preventive strategies in clinical care. Full article

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

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23 pages, 4171 KiB

Open AccessArticle

Composite Probiotics Improve Gut Health and Enhance Tryptophan Metabolism in Nursery Piglets During Liquid Feeding

by Man Du, Qifan Zhang, Yutian Shen, Jie Fu, Yizhen Wang, Bin Yao and Zeqing Lu

Int. J. Mol. Sci. 2025, 26(12), 5698; https://doi.org/10.3390/ijms26125698 (registering DOI) - 13 Jun 2025

Abstract

Probiotics are widely used as dietary additives to strengthen gut barrier function, shape microbiota composition, regulate host metabolism, and promote overall health. To enhance probiotic delivery and microbial viability, this study evaluated a liquid feeding system supplemented with a probiotic consortium (Bifidobacterium [...] Read more.

Probiotics are widely used as dietary additives to strengthen gut barrier function, shape microbiota composition, regulate host metabolism, and promote overall health. To enhance probiotic delivery and microbial viability, this study evaluated a liquid feeding system supplemented with a probiotic consortium (Bifidobacterium infantis, Lactobacillus plantarum, and Pediococcus acidilactici) in nursery piglets. A 60-day trial involving 270 piglets (16.84 ± 0.12 kg) compared three diets: solid feed (Dry), liquid feed (Liq), and probiotic-enriched liquid feed (Pro). Compared to the Dry and Liq groups, probiotic supplementation significantly improved growth performance, with the average daily gain increasing by over 17.86% (p < 0.01) and the average daily feed intake increasing by more than 6.08% (p < 0.05). The feed conversion ratio was reduced by up to 8.08% (p < 0.05), indicating improved feed efficiency. The Pro group also exhibited elevated tight junction protein expression (p < 0.05), increased colonic short-chain fatty acid levels (p < 0.01), and decreased serum biomarkers of intestinal permeability (p < 0.05). The 16 S rRNA sequencing indicated the probiotic-driven colonization of B. infantis and L. plantarum and the suppression of opportunistic pathogens. Metabolomic analyses revealed enhanced colonic tryptophan metabolism, evidenced by elevated kynurenic and xanthurenic acid levels. Additionally, serum-targeted metabolomics and in vitro experiments confirmed that B. infantis and L. plantarum effectively converted tryptophan into indole-3-lactic acid, promoting its accumulation in piglet serum and colons. These results deepen our understanding of the mechanisms by which probiotics and tryptophan metabolism enhance intestinal health, providing a foundational platform for the application of probiotic-based interventions in livestock production. Full article

(This article belongs to the Special Issue Beyond Digestion: The Role of Gut Microbiota in Metabolism, Immunity and Brain Function)

19 pages, 6083 KiB

Open AccessArticle

Bioprospecting for Anti-Kinetoplastid Drug Discovery from Aloysia citrodora Essential Oil

by Amani Omrani, Meriam Ben Youssef, Ines Sifaoui, Eduardo Hernández-Álvarez, María J. Trujillo-Rodríguez, Montse Saura-Cayuela, Verónica Pino, Hichem Sebai, Isabel L. Bazzocchi, Jacob Lorenzo-Morales, José E. Piñero and Ignacio A. Jiménez

Int. J. Mol. Sci. 2025, 26(12), 5697; https://doi.org/10.3390/ijms26125697 (registering DOI) - 13 Jun 2025

Abstract

Natural products have long been recognized as invaluable resources in drug discovery. Essential oils have attracted widespread attention due to their broad spectrum of biological activities. Herein, we report the anti-kinetoplastid activity of Aloysia citrodora leaf essential oil through a bioassay-guided fractionation method [...] Read more.

Natural products have long been recognized as invaluable resources in drug discovery. Essential oils have attracted widespread attention due to their broad spectrum of biological activities. Herein, we report the anti-kinetoplastid activity of Aloysia citrodora leaf essential oil through a bioassay-guided fractionation method against the etiological agents of Chagas disease and leishmaniasis. This approach has led to the isolation and structural identification of compound 1 (citral) as the main active constituent, with IC₅₀ values of 8.47 μM against Leishmania amazonensis and 12.90 μM against Trypanosoma cruzi. In addition, eight compounds (2–9) were synthesized and evaluated. Among these, citral 2,4-dinitrophenylhydrazone (9) exhibited the highest anti-kinetoplastid activity, with an IC₅₀ value of 10.62 μM against L. amazonensis, displaying a similar biological profile to citral and the reference drug. Structure–activity relationship studies revealed that the type of Schiff base and acylating agent played a crucial role in the activity. Mechanism of action studies demonstrated that compound 9 directly targets the apoptotic pathway, inducing programmed cell death through selective pathway inhibition. This work underscores the potential of A. citrodora essential oil and its compounds as prospective therapeutic leads against neglected tropical diseases. Full article

(This article belongs to the Special Issue Biological Research on Plant Bioactive Compounds)

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24 pages, 9006 KiB

Open AccessArticle

X-Ray Exposure Induces Structural Changes in Human Breast Proteins

by Ren Jie Tuieng, Sarah H. Cartmell, Cliona C. Kirwan, Alexander Eckersley and Michael J. Sherratt

Int. J. Mol. Sci. 2025, 26(12), 5696; https://doi.org/10.3390/ijms26125696 (registering DOI) - 13 Jun 2025

Abstract

During radiotherapy, X-rays can deliver significant doses of ionising radiation to both cancerous and healthy tissue, often leading to undesirable side effects that compromise patient outcomes. While the cellular effects of such therapeutic X-ray exposures are well studied, the impact on extracellular matrix [...] Read more.

During radiotherapy, X-rays can deliver significant doses of ionising radiation to both cancerous and healthy tissue, often leading to undesirable side effects that compromise patient outcomes. While the cellular effects of such therapeutic X-ray exposures are well studied, the impact on extracellular matrix (ECM) proteins remains poorly understood. This study characterises the response of ECM proteins, including the major tissue components collagen I and fibronectin (FN), to X-ray doses similar to those used in clinical practice (50 Gy, as employed in breast radiotherapy, and 100 Gy), using a combination of gel electrophoresis, biochemical assays, and mass spectrometry-based peptide location fingerprinting (PLF) analysis. In purified protein solutions, 50 Gy X-ray exposure led to the fragmentation of constituent collagen I α chains. Irradiation of purified plasma FN (pFN) induced localised changes in peptide yields (detected by liquid chromatography and tandem mass spectrometry (LC-MS/MS) and PLF) and enhanced its binding to collagen I. In complex environments, such as newly synthesised fibroblast-derived ECM and mature ex vivo breast tissue, X-ray exposure induced peptide yield changes in not only collagen I and FN but also key basement membrane proteins, including collagen IV, laminin, and perlecan. Intracellular proteins associated with gene expression (RPS3, MeCP2), the cytoskeleton (moesin, plectin), and the endoplasmic reticulum (calnexin) were also found to be impacted. These X-ray-induced structural changes may impair the ECM integrity and alter cell–ECM interactions, with potential implications for tissue stiffening, fibrosis, and impaired wound healing in irradiated tissues. Full article

(This article belongs to the Special Issue Novel Molecular and Cellular Biology Approaches in the Assessment of Radiation Effects)

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Open AccessArticle

Free and Bioavailable Vitamin D Are Correlated with Disease Severity in Acute Pancreatitis: A Single-Center, Prospective Study

by Darko Siuka, Matej Rakuša, Aleš Vodenik, Lana Vodnik, Borut Štabuc, David Štubljar, David Drobne, Aleš Jerin, Helena Matelič and Joško Osredkar

Int. J. Mol. Sci. 2025, 26(12), 5695; https://doi.org/10.3390/ijms26125695 - 13 Jun 2025

Abstract

Acute pancreatitis (AP) is primarily caused by inflammation and immunological responses, both of which are regulated by vitamin D. The purpose of this study was to examine the correlation between the severity of AP and vitamin D levels, including its total, free, and [...] Read more.

Acute pancreatitis (AP) is primarily caused by inflammation and immunological responses, both of which are regulated by vitamin D. The purpose of this study was to examine the correlation between the severity of AP and vitamin D levels, including its total, free, and bioavailable forms. Eighty individuals with AP were enrolled in this study. Serum levels of free 25(OH)D₃, bioavailable 25(OH)D₃, and total 25-hydroxyvitamin D 25(OH)D₃ were assessed. The severity of the disease course was assessed by scoring systems (Revised Atlanta classification, Ranson score, CTSI). Vitamin D deficiency was common in AP patients, with 31.3% being categorized as deficient (<50 nmol/L) and 27.5% having a severe deficiency (<30 nmol/L). Compared to patients with adequate vitamin D status, those with lower vitamin D levels had a significantly higher risk of developing moderate-to-severe AP (44.7% vs. 14.3%, p = 0.029). Patients with severe vitamin D insufficiency were the only ones who experienced severe AP. Clinical outcomes showed similar correlations: patients with significant vitamin D deficiency had longer hospital stays (mean of 12.1 ± 5.3 days vs. 7.8 ± 3.4 days, p = 0.018) and higher rates of ICU admission (31.8% vs. 8.0%, p = 0.007). Low levels of total, free, and bioavailable vitamin D were significantly associated with the severity of AP and ICU admission. Free, bioavailable, and total vitamin D were correlated with the severity of acute pancreatitis. All severe cases occurred in patients with severe vitamin D deficiency. Given the observational design, these associations require confirmation in interventional or mechanistic studies. Full article

(This article belongs to the Section Bioactives and Nutraceuticals)

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Int. J. Mol. Sci., Volume 26, Issue 12 (June-2 2025) – 299 articles

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