International Journal of Molecular Sciences

26 pages, 10327 KB

Open AccessArticle

Roflumilast Inhibits Fibrogenic Activation in Human Intestinal Myofibroblasts via Inhibition of Myocardin-Related Transcription Factor/Serum Response Factor Signaling

by Dongju Lee, Yoon Jeong Choi, In Kyung Yoo, Jeonghee Han, Duk Hwan Kim, Jee Hyun Kim and Jun Hwan Yoo

Int. J. Mol. Sci. 2026, 27(16), 7126; https://doi.org/10.3390/ijms27167126 (registering DOI) - 8 Aug 2026

Abstract

The lack of effective anti-fibrotic agents remains a significant unmet need in the treatment of intestinal fibrosis, a condition largely driven by transforming growth factor-β1 (TGF-β1)-mediated myofibroblast activation. Phosphodiesterase 4 (PDE4) inhibitors, known to increase intracellular cAMP levels, exhibit anti-inflammatory and potential anti-fibrotic [...] Read more.

The lack of effective anti-fibrotic agents remains a significant unmet need in the treatment of intestinal fibrosis, a condition largely driven by transforming growth factor-β1 (TGF-β1)-mediated myofibroblast activation. Phosphodiesterase 4 (PDE4) inhibitors, known to increase intracellular cAMP levels, exhibit anti-inflammatory and potential anti-fibrotic properties, though their efficacy in intestinal fibrosis is poorly defined. In this study, we investigated the anti-fibrotic effects and underlying mechanisms of PDE4 inhibitors (rolipram, roflumilast, piclamilast, and mesopram) in human intestinal myofibroblasts (HIMFs) stimulated with TGF-β1. All PDE4 inhibitors significantly reduced TGF-β1-induced mRNA expression of collagen1A1 (COL1A1) and fibronectin (FN1), with mesopram additionally reducing α-smooth muscle actin (ACTA2) mRNA expression. At the protein level, however, only roflumilast significantly decreased procollagen1A1 (Procol1A1) and FN expression. Mechanistically, roflumilast, rolipram, and mesopram significantly reduced serum response factor (SRF) mRNA expression, whereas piclamilast and mesopram significantly inhibited myocardin-related transcription factor A (MRTFA) mRNA expression. Rolipram and roflumilast exhibited a decreasing trend in MRTFA mRNA expression without statistical significance. Notably, roflumilast demonstrated superior inhibitory effects, significantly decreasing both MRTF-A and SRF protein expression and effectively reducing nuclear localization of MRTF-A. Additionally, rolipram and roflumilast significantly attenuated TGF-β1-induced phosphorylation of Smad2. These findings indicate that PDE4 inhibitors, particularly roflumilast, effectively suppress TGF-β1-induced fibrogenic activation in HIMFs by modulating MRTF/SRF and Smad-dependent pathways, highlighting the value of roflumilast for further preclinical investigation as a potential therapeutic strategy for intestinal fibrosis. Full article

(This article belongs to the Special Issue Skin Extracellular Matrix and Basement Membrane)

31 pages, 2726 KB

Open AccessReview

From Oilseed Waste to High-Value Bioactives: Deep Eutectic Solvents as Sustainable Refining Media

by Marcelina Mazur, Kristina Radošević, Marina Cvjetko Bubalo, Višnja Gaurina Srček and Ivana Radojčić Redovniković

Int. J. Mol. Sci. 2026, 27(16), 7125; https://doi.org/10.3390/ijms27167125 (registering DOI) - 8 Aug 2026

Abstract

The global oil-processing industry generates substantial quantities of by-products and secondary streams, including oilseed cakes, pomaces, hulls, and wastewaters, which remain largely underutilized despite being rich sources of high-value bioactive compounds. The development of sustainable strategies for the valorization of these residues is [...] Read more.

The global oil-processing industry generates substantial quantities of by-products and secondary streams, including oilseed cakes, pomaces, hulls, and wastewaters, which remain largely underutilized despite being rich sources of high-value bioactive compounds. The development of sustainable strategies for the valorization of these residues is increasingly recognized as a key component of circular bioeconomy and biorefinery frameworks. In this context, deep eutectic solvents (DESs) have attracted considerable attention as a new generation of designer solvents owing to their tunable physicochemical properties, low vapor pressure, ease of synthesis, and potential environmental compatibility. This review critically discusses the current state of knowledge regarding the application of DESs in the processing and valorization of oil industry by-products. Particular emphasis is placed on the relationship between DES composition, physicochemical characteristics, and extraction performance. Recent advances in the recovery of phenolic compounds, proteins, saccharides, and tocopherols from oilseed-derived residues are comprehensively examined, including the integration of DESs with intensified extraction techniques such as microwave-, ultrasound-, and ohmic-assisted extraction. Furthermore, the role of DESs in oil purification processes and the treatment of technological waste stream is evaluated. Emerging evidence indicates that DES-based systems not only enhance extraction efficiency and selectivity but may also improve the stability, bioaccessibility, and purity of the recovered compounds. Finally, the opportunities and challenges associated with the implementation of DES-based technologies within integrated biorefinery schemes are discussed, including solvent recovery, product scalability, sensory acceptability, and regulatory considerations. The available literature demonstrates that DESs constitute a versatile platform for the sustainable valorization of oil-processing residues, supporting the transition from conventional waste management approaches toward resource-efficient and circular production systems. Full article

(This article belongs to the Special Issue Bioactives from Natural Products)

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20 pages, 2340 KB

Open AccessReview

From Cloning Vectors to Phage Display: Engineering Principles and Translational Applications of Bacteriophage Display Platforms

by Tingting Hong, Nan Chen, Yingli Yang, Yao Wang, Yao Yao and Caihong Zheng

Int. J. Mol. Sci. 2026, 27(16), 7124; https://doi.org/10.3390/ijms27167124 (registering DOI) - 8 Aug 2026

Abstract

Bacteriophage technologies have evolved from classical cloning vectors into programmable platforms for genome engineering and molecular selection. Phage display couples a surface-presented binding phenotype to its encoding genotype, enabling iterative selection, sequence recovery, and optimization of peptides, antibody fragments, and other protein binders. [...] Read more.

Bacteriophage technologies have evolved from classical cloning vectors into programmable platforms for genome engineering and molecular selection. Phage display couples a surface-presented binding phenotype to its encoding genotype, enabling iterative selection, sequence recovery, and optimization of peptides, antibody fragments, and other protein binders. This review links phage morphology, genome organization, infection strategy, host defense, and engineering method to practical platform choice. It compares λ, N15, M13, and T7 systems; examines biopanning bias and candidate developability; and evaluates artificial intelligence-assisted, sequencing-guided, and structure-guided workflows. Vaccine applications are considered alongside constraints arising from anti-phage immunity, antigen density, route of administration, and repeat dosing. Progress will depend on experimentally validated closed-loop workflows that integrate library design, selection, high-throughput analytics, structural characterization, and early manufacturability assessment. Full article

(This article belongs to the Special Issue Applications of Bacteriophages)

21 pages, 3172 KB

Open AccessReview

Ultra-Processed Diets and Pediatric Acne: Insulin–mTOR Activation and Its Potential Role in Cutaneous Inflammation

by Yasmeen Magharehabed, Zainab Ibrahim, Hesham Shiekhtholth and Nabiha Yusuf

Int. J. Mol. Sci. 2026, 27(16), 7123; https://doi.org/10.3390/ijms27167123 (registering DOI) - 8 Aug 2026

Abstract

Acne vulgaris is an inflammatory cutaneous condition that disproportionately affects the pediatric population. While there are several risk factors, emerging evidence suggests that ultra-processed foods (UPFs), as part of Western dietary patterns, may contribute to acne pathophysiology through activation of inflammatory pathways, such [...] Read more.

Acne vulgaris is an inflammatory cutaneous condition that disproportionately affects the pediatric population. While there are several risk factors, emerging evidence suggests that ultra-processed foods (UPFs), as part of Western dietary patterns, may contribute to acne pathophysiology through activation of inflammatory pathways, such as mTORC1. This comprehensive review synthesizes current evidence regarding acne pathogenesis in conjunction with diet-associated inflammatory cascades to better illustrate the potential role of diet as an adjunct to clinical management in pediatric patients. The current literature suggests that increased insulin/IGF-1 levels may contribute to alterations in the skin and gut microbiota. Additionally, components commonly found in UPFs have been proposed to activate the mechanistic target of rapamycin complex (mTORC1) through insulin/IGF-1-dependent and -independent mechanisms, perpetuating inflammatory pathways that give rise to acne pathogenesis. However, the majority of available evidence is derived from adult cohorts; pediatric-specific evidence remains limited. While studies have demonstrated clinical significance in acne severity with dietary interventions, future high-quality studies are required. Through understanding the relationship between diet and acne pathogenesis, future therapeutic and preventative strategies may be developed to improve pediatric acne clinical outcomes. Full article

(This article belongs to the Special Issue Molecular Research on Skin Inflammation (2nd Edition))

26 pages, 3903 KB

Open AccessArticle

From Descriptor Learning to Binding Stability: An Explainable Machine Learning Pipeline for EGFR Double-Mutant Inhibitor Discovery

by Jurica Novak

Int. J. Mol. Sci. 2026, 27(16), 7122; https://doi.org/10.3390/ijms27167122 (registering DOI) - 8 Aug 2026

Abstract

Drug resistance arising during cancer development and progression remains a major challenge in the treatment of epidermal growth factor receptor (EGFR)-driven tumors, particularly those harboring the clinically relevant T790M/L858R double mutation. In this study, we developed an integrated computational workflow combining explainable machine [...] Read more.

Drug resistance arising during cancer development and progression remains a major challenge in the treatment of epidermal growth factor receptor (EGFR)-driven tumors, particularly those harboring the clinically relevant T790M/L858R double mutation. In this study, we developed an integrated computational workflow combining explainable machine learning, virtual screening, molecular dynamics simulations, and binding free-energy calculations to identify novel inhibitors of this drug-resistant EGFR variant. An XGBoost regression model was trained using scaffold-aware cross-validation, Bayesian hyperparameter optimization, and sequential feature selection, resulting in a compact model based on 16 molecular descriptors. The model demonstrated robust predictive performance on external validation data, while SHAP analysis identified descriptors related to the local electronic environment, fragment distribution, and molecular topology as the primary contributors to activity prediction. The optimized model was subsequently applied to screen compounds from the Enamine REAL database. Top-ranked candidates were evaluated using explicit-solvent molecular dynamics simulations and MM/GBSA binding free-energy calculations. Several compounds formed stable protein–ligand complexes and maintained key interactions with residues known to be important for EGFR inhibition, including Lys745, Met790, and Leu718. These results demonstrate that the proposed workflow can efficiently prioritize computational candidates of drug-resistant EGFR mutants and may support the development of new therapeutic strategies for overcoming resistance in EGFR-driven cancers. Full article

(This article belongs to the Special Issue Developmental Biology: Computational and Experimental Approaches, 3rd Edition)

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15 pages, 3810 KB

Open AccessArticle

The Genetic Structure of the Romanian Male Population Revealed by 27 Y-Chromosome STR Loci

by George Popoiu, Florin Stanciu, Paulina Popescu, Veronica Cuțăr, Simona Vladu, Violeta Nicola, Anastasia Procopciuc, Ana Rădulescu, Adnana Cotolea and Sergiu Emil Georgescu

Int. J. Mol. Sci. 2026, 27(16), 7121; https://doi.org/10.3390/ijms27167121 (registering DOI) - 8 Aug 2026

Abstract

Y-chromosomal Short Tandem Repeats (Y-STRs) provide insight into forensic evidence interpretation and male population history. Romania’s position at the crossroads of Europe and Western Asia makes it a key reference population for both domains, yet existing Romanian Y-STR databases are limited in geographic [...] Read more.

Y-chromosomal Short Tandem Repeats (Y-STRs) provide insight into forensic evidence interpretation and male population history. Romania’s position at the crossroads of Europe and Western Asia makes it a key reference population for both domains, yet existing Romanian Y-STR databases are limited in geographic coverage and marker number. We genotyped 928 unrelated Romanian males across all 41 counties and Bucharest at 27 Y-STR loci using the Investigator Argus Y-28 Kit, and modeled haplotype frequencies using the Discrete Laplace (DL) distribution (disclapmix v1.7.5, 17-locus panel; disclapmix2 v0.6.1, 27-locus panel). Discrete Laplace modeling revealed 12 and 14 optimal mixture components for the 17- and 27-locus models, respectively, with median match probabilities of 1 in 1.25 × 10⁷ and 1 in 5.8 × 10¹², reflecting nearly six order-of-magnitude gain in evidential weight. Haplogroup analysis identified 16 Y-lineages; R1a, I2a, E1b1b, J2a, and R1b collectively represent ~80% of the population, and reflect Romania’s layered Steppe, Balkan, and Near Eastern ancestry, with subtle regional gradients between Moldavia, Transylvania, and Muntenia. This dataset provides validated forensic reference data and new insights into the patrilineal genetic structure of the Romanian population. Full article

(This article belongs to the Special Issue Research Progress of Forensic Genetics)

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23 pages, 7434 KB

Open AccessArticle

Heterogeneous CRISPR/Cas9 Editing of HMOX1 Is Associated with Altered Heme–Biliverdin Metabolism and Basal Stress-Associated Transcriptional Programs in Chicken LMH Cells

by Haonan Tang, Huaiyu Li, Yurong Tai, Xue Yang, Letian Zhang, Yuhao Ma, Ganxian Cai, Hongyang Zhao, Tong Zeng, Xiaohua Ai, Shuang He, Jiankui Wang, Zhiliang Gu and Xuemei Deng

Int. J. Mol. Sci. 2026, 27(16), 7120; https://doi.org/10.3390/ijms27167120 (registering DOI) - 8 Aug 2026

Abstract

Heme oxygenase-1 (HO-1), encoded by HMOX1, catalyzes the rate-limiting step of heme degradation and generates biliverdin, carbon monoxide, and ferrous iron, thereby linking heme turnover with redox regulation and stress-associated signaling. In birds, biliverdin is retained as a major heme-derived product, but [...] Read more.

Heme oxygenase-1 (HO-1), encoded by HMOX1, catalyzes the rate-limiting step of heme degradation and generates biliverdin, carbon monoxide, and ferrous iron, thereby linking heme turnover with redox regulation and stress-associated signaling. In birds, biliverdin is retained as a major heme-derived product, but the cellular consequences of HMOX1 perturbation remain insufficiently defined. Here, CRISPR/Cas9-mediated editing was used to generate a heterogeneous HMOX1-edited population in Chicken hepatocellular carcinoma-derived cells. The selected sgRNA reduced HO-1 protein abundance by approximately 47%, and no detectable cleavage was observed at the seven predicted high-risk off-target loci examined. Compared with vector-control cells, HMOX1-edited cells exhibited intracellular heme accumulation, reduced biliverdin levels, increased oxidation-sensitive fluorescence, and reduced CCK-8 absorbance values, indicating disruption of heme–biliverdin metabolic and redox homeostasis. RNA sequencing identified 2650 differentially expressed genes, including 951 upregulated and 1699 downregulated genes. Downregulated genes were mainly enriched in immune, cytokine, MAPK/stress, and extracellular signaling-associated pathways, whereas DNA replication and cell-cycle-related genes were increased. Enrichment-term association and STRING functional-association analyses further identified a coordinated module involving IL1B, JUN, NFKBIA, IRF1, TGFB1, IL10, CCL5, and PTGS2. Independent RT-qPCR analysis confirmed selected expression trends. These findings show that heterogeneous HMOX1 editing and reduced HO-1 abundance are associated with disruption of the avian heme–biliverdin metabolic axis and coordinated remodeling of basal immune, stress, extracellular signaling, and cell-cycle-associated transcriptional programs in Chicken hepatocellular carcinoma-derived cells. Full article

(This article belongs to the Special Issue Decoding Animal Reproduction: From Molecular Mechanisms to Breeding Innovations)

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25 pages, 817 KB

Open AccessReview

Rewiring the Molecular Interplay of CDK4/6 Inhibitors in Lung Cancer: From Cell Cycle Control to Immune Microenvironment Remodeling

by Yin Ku, Yao Zheng, Yu Ding, Peichuan Zhang, Xiaoqing Wu and Yaohui Chen

Int. J. Mol. Sci. 2026, 27(16), 7119; https://doi.org/10.3390/ijms27167119 (registering DOI) - 8 Aug 2026

Abstract

Traditional inhibitors of cyclin-dependent kinases 4 and 6 (CDK4/6) have long been characterized as classical antiproliferative agents that induce G1 cell cycle arrest by blocking the phosphorylation of the retinoblastoma protein (Rb). However, recent studies in lung cancer have expanded this paradigm, revealing [...] Read more.

Traditional inhibitors of cyclin-dependent kinases 4 and 6 (CDK4/6) have long been characterized as classical antiproliferative agents that induce G1 cell cycle arrest by blocking the phosphorylation of the retinoblastoma protein (Rb). However, recent studies in lung cancer have expanded this paradigm, revealing a functional transition from exclusive tumor suppression to the profound remodeling of the tumor microenvironment (TME) to enhance antitumor immunity. This review systematically outlines the genomic aberrations of the CDK4/6-Rb axis across lung cancer subtypes and dissects its immunomodulatory networks. These encompass the activation of effector T cells, the alleviation of immunosuppression mediated by regulatory T cells (Tregs), and the enhancement of antigen presentation via the Cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway. Furthermore, we analyze acquired resistance mechanisms, primarily focusing on p21-CDK2 bypass activation mediated by Cyclin E1 gene (CCNE1) amplification and tumor protein 53 gene (TP53) mutations. We also review clinical investigations combining CDK4/6 inhibitors with targeted therapies against driver genes, as well as immune checkpoint inhibitors in lung cancer. Notably, in the context of lung cancer, these combinatorial strategies have been primarily investigated in the second-line or subsequent settings following progression on standard platinum-based chemotherapy or immunotherapy. Finally, we propose individualized, stratified treatment strategies based on genomic and immunological biomarkers, providing a translational framework for overcoming multidrug resistance and optimizing next-generation combinatorial regimens in lung cancer. Full article

(This article belongs to the Special Issue Targeted Anticancer Therapeutics: Mechanisms, Resistance, Tumor Microenvironment, and Translational Advances)

24 pages, 764 KB

Open AccessReview

Beneficial Hepatokines in MASLD/MASH: Therapeutic Potentials and Drug Delivery Challenges

by Reeju Amatya, Kyoung Ah Min and Meong Cheol Shin

Int. J. Mol. Sci. 2026, 27(16), 7118; https://doi.org/10.3390/ijms27167118 (registering DOI) - 8 Aug 2026

Abstract

Metabolic dysfunction-associated steatotic liver disease (MASLD) and its progressive form, metabolic dysfunction-associated steatohepatitis (MASH), are a growing global health burden with extremely limited pharmacological options, thereby indicating an urgent need for innovative therapeutic strategies. Hepatokines are liver-derived secreted proteins that coordinate metabolic communication [...] Read more.

Metabolic dysfunction-associated steatotic liver disease (MASLD) and its progressive form, metabolic dysfunction-associated steatohepatitis (MASH), are a growing global health burden with extremely limited pharmacological options, thereby indicating an urgent need for innovative therapeutic strategies. Hepatokines are liver-derived secreted proteins that coordinate metabolic communication between the liver and peripheral organs and have emerged as mechanistically compelling therapeutic candidates. This review comprehensively examines beneficial hepatokines with protective roles in MASLD/MASH, detailing their molecular mechanisms of action across key metabolic tissues, including their effects on hepatic lipid metabolism, insulin sensitivity, inflammatory signaling, and fibrogenesis. We further discuss the fundamental pharmacokinetic barriers of these protein therapeutics, particularly their susceptibility to renal clearance and proteolytic degradation. Furthermore, we examine the principal half-life extension strategies to overcome these limitations, with particular emphasis on their clinical application to FGF21-based drug candidates that are currently advancing through phase 3 trials. Overall, this review highlights the therapeutic potential of hepatokine-based biologics and the critical role of protein engineering in translating these mechanistic insights into durable, clinically viable treatments for MASLD/MASH. Full article

(This article belongs to the Special Issue Targeted Peptide Drugs for Metabolic Diseases)

35 pages, 3771 KB

Open AccessArticle

Multifunctional Electrospun PCL/Starch/n-Al₂O₃ Nanocomposites: Potential Antibacterial Wound Dressing Applications

by Felipe Gutiérrez, Diana Zárate-Triviño, Francisco A. Cataño, Alexander Córdoba, Marcela Saavedra, Esmeralda López, Aline Alfaro, Eliana Rodríguez, Jennifer Leos, Sebastián Zapata, Pedro Orihuela and Paula A. Zapata

Int. J. Mol. Sci. 2026, 27(16), 7117; https://doi.org/10.3390/ijms27167117 (registering DOI) - 8 Aug 2026

Abstract

Multifunctional polymer scaffolds with mechanical support, biocompatibility, and antimicrobial activity are key for next-generation biomedical materials. We report the fabrication of electrospun nanocomposite fibers made from polycaprolactone (PCL), starch, and mesoporous aluminum oxide nanoparticles (n-Al₂O₃). Nanoparticles (11 ± 4 [...] Read more.

Multifunctional polymer scaffolds with mechanical support, biocompatibility, and antimicrobial activity are key for next-generation biomedical materials. We report the fabrication of electrospun nanocomposite fibers made from polycaprolactone (PCL), starch, and mesoporous aluminum oxide nanoparticles (n-Al₂O₃). Nanoparticles (11 ± 4 nm) were synthesized via a sol-gel method, predominantly comprising γ- and α-Al₂O₃ phases. Four fiber systems were fabricated by side-by-side electrospinning: PCL, PCL/starch, PCL/n-Al₂O₃, and PCL/starch/n-Al₂O₃. SEM analysis confirmed uniform and bead-free fibers in all formulations. Tensile tests showed that the incorporation of starch and nanoparticles improved the mechanical performance compared with neat PCL. In particular, PCL/starch/n-Al₂O₃ fibers exhibited increases of 404% in Young’s modulus and 102% in elongation at break. In PBS, starch and n-Al₂O₃ enhanced hydrophilicity and accelerated weight loss, with PCL/starch/n-Al₂O₃ showing the highest mass loss. Antibacterial tests indicated that only fibers with nanoparticles could inhibit Staphylococcus aureus and Escherichia coli, with PCL/starch/n-Al₂O₃ showing a major effect. Although n-Al₂O₃ increased cytotoxicity toward NIH-3T3, starch mitigated this effect, and the ternary scaffold showed no detectable cytotoxicity. Moreover, PCL/starch/n-Al₂O₃ exhibited non-hemolytic behavior, enhanced fibroblast migration, and wound-healing-related protein expression. Overall, side-by-side electrospun PCL/starch/n-Al₂O₃ scaffold exhibited showed improved mechanical, biological, and antibacterial properties, supporting its potential as a wound-dressing material. Full article

(This article belongs to the Special Issue Synthesis Manufacturing and Biomedical Applications of Nanofibers Scaffold)

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11 pages, 269 KB

Open AccessArticle

EGPA at Diagnosis: A Comprehensive Single-Center Profile of Laboratory Findings and Clinical Evidence

by Silvia Brunetto, Francesca Dimasi, Cristiano Maiolo, Emanuela Zumbo, Federica Buta, Sebastiano Gangemi and Luisa Ricciardi

Int. J. Mol. Sci. 2026, 27(16), 7116; https://doi.org/10.3390/ijms27167116 (registering DOI) - 8 Aug 2026

Abstract

Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare vasculitis. A key bio-logical hallmark is peripheral blood eosinophilia while antineutrophil cytoplasmic an-tibody (ANCA) positivity is not always present. Therefore, an early phase suspicion of EGPA leading to a correct diagnosis can be challenging. We [...] Read more.

Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare vasculitis. A key bio-logical hallmark is peripheral blood eosinophilia while antineutrophil cytoplasmic an-tibody (ANCA) positivity is not always present. Therefore, an early phase suspicion of EGPA leading to a correct diagnosis can be challenging. We performed an observa-tional cross-sectional study limited to baseline data on 38 patients between December 2019 and December 2025 at the Allergy and Clinical Immunology Unit, Messina, Italy. Data collection included eosinophil, neutrophil, and lymphocyte counts; ANCAs and antinuclear antibodies (ANAs); erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) determination; and the Birmingham vasculitis activity score (BVAS) questionnaire: Median eosinophil counts were 685 cells/µL, the neutro-phil-to-lymphocyte ratio (NLR) was 2.29, ESR median values were 24 mm/h, and CRPs were 1.99 mg/L. ANCAs were positive in five patients, and ANAs in 20. The trend in ANA+ patients was of lower median eosinophil counts and higher ESR and CRP me-dian values and median BVASs. General, nervous system, and ENT BVAS domains had higher scores.: Disease activity in EGPA at diagnosis can be difficult to recognize. We defined it as chameleon-like and could not be captured by specific immunological sig-natures. Therefore, an early diagnosis needs multidimensional assessment, integrating laboratory parameters with clinical scores. In our EGPA cohort, ANAs were detected in just over half the patients, suggesting that rather than acting as bystanders, these could help clinicians, together with eosinophil counts, NLRs, and BVASs, to suspect EGPA at an early stage for referral to specialized medical centers. Full article

16 pages, 2909 KB

Open AccessArticle

Altered Embryonic SIRT6 and SIRT7 Expression Is Associated with Impaired Developmental Competence and Oocyte-Dependent Embryo Quality in Embryos Derived from Subfertile Males

by Alicja Kowalczyk, Mercedes Camiña García, José Ángel Hernández Malagón, Jose Pedro Araujo, Ivona Žura Žaja, Marko Pećin, Dražen Đuričić, Elżbieta Gałęska, Zbigniew Dobrzański and Marko Samardžija

Int. J. Mol. Sci. 2026, 27(16), 7115; https://doi.org/10.3390/ijms27167115 (registering DOI) - 8 Aug 2026

Abstract

Paternal contributions to preimplantation embryo development are increasingly recognized as an important component of reproductive success, but the associations between male reproductive phenotype, early embryonic competence, and embryo molecular characteristics remain insufficiently defined. Using bovine in vitro embryo production as a translational large-mammalian [...] Read more.

Paternal contributions to preimplantation embryo development are increasingly recognized as an important component of reproductive success, but the associations between male reproductive phenotype, early embryonic competence, and embryo molecular characteristics remain insufficiently defined. Using bovine in vitro embryo production as a translational large-mammalian model, this study evaluated whether paternal reproductive phenotype and oocyte origin were associated with embryo developmental performance and embryonic sirtuin expression. Oocytes obtained from mature cows or heifers were fertilized with semen from bulls differing in reproductive status, including bulls characterized by libido disturbances and irregular semen collection. Fertilization, cleavage, blastocyst formation, and hatching were assessed, while embryonic SIRT2, SIRT3, SIRT6, and SIRT7 expression was quantified by immunofluorescence. Early developmental endpoints were relatively preserved, whereas differences were more evident at later stages of preimplantation development. Cow-derived oocytes were associated with higher hatching rates than heifer-derived oocytes. Embryos generated using semen from bulls with an impaired reproductive phenotype showed lower developmental competence and lower SIRT6 and SIRT7 expression. SIRT6 expression showed the strongest positive correlation with hatching, and positive correlations were also observed among the analyzed sirtuins. These findings indicate that paternal reproductive phenotype and oocyte origin are associated with bovine embryo developmental competence and embryonic sirtuin profiles. Embryonic SIRT6 and SIRT7 expression may represent candidate molecular indicators of embryo competence; however, causal relationships cannot be inferred from the present study design. Full article

(This article belongs to the Special Issue Female and Male Fertility: From Diseases to Current Trends and Research Developments)

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31 pages, 2565 KB

Open AccessReview

Single-Cell and Spatial Omics Technologies in Rice Abiotic Stress Biology: A Methodological Review

by Junxiao Chen, Zheng Chen, Chun Yin, Lei Zhou and Da Zhao

Int. J. Mol. Sci. 2026, 27(16), 7114; https://doi.org/10.3390/ijms27167114 (registering DOI) - 8 Aug 2026

Abstract

Abiotic stresses—drought, salinity, extreme temperature, flooding, and heavy-metal toxicity—constrain rice (Oryza sativa L.) yield worldwide, and the cellular programmes underlying them are unevenly distributed across cell types that bulk-tissue assays average together. This review examines, from a methodological standpoint, what single-cell and [...] Read more.

Abiotic stresses—drought, salinity, extreme temperature, flooding, and heavy-metal toxicity—constrain rice (Oryza sativa L.) yield worldwide, and the cellular programmes underlying them are unevenly distributed across cell types that bulk-tissue assays average together. This review examines, from a methodological standpoint, what single-cell and spatial omics technologies can and cannot establish about rice abiotic stress biology. We first define the modality space: single-cell omics measures RNA, chromatin accessibility, DNA methylation, protein, or metabolite features at the resolution of individual cells or nuclei, whereas spatial omics measures such features while retaining tissue coordinates; the two are complementary rather than interchangeable. We then treat each platform class—droplet-based scRNA-seq, combinatorial-indexing approaches including SPLiT-seq, nuclei-based snRNA-seq and multiome, sequencing-based and imaging-based spatial transcriptomics—under a common template covering measurement principle, the questions each can answer, applicability to rice tissues, dominant biases, and the inferences each cannot support. To make evidence strength comparable across a heterogeneous literature, we apply a four-tier scheme throughout: Tier A, direct rice cell-resolved or spatial evidence with functional or field validation; Tier B, robust rice functional and localization evidence without single-cell data; Tier C, cell-resolved evidence without causal validation; and Tier D, cross-species analogy or reasoned proposal. Applying this scheme shows that the genes with genuine breeding traction in rice—SUB1A, OsHKT1;5, OsHMA3, OsNRAMP5, DRO1—rest on Tier B evidence from classical genetics and field testing, whereas the most cell-resolved rice evidence concentrates in root outer layers and barrier formation at Tier C, and heat and cold stress, despite dominating yield loss, lack rice cell-resolved data almost entirely. We extend the discussion beyond transcriptomics to single-cell DNA methylome profiling, spatial proteomics and metabolomics, and three-dimensional analysis of thick plant tissues, in each case distinguishing demonstrated plant capability from mammalian-only capability, and we assess the expanding role of artificial intelligence in annotation, segmentation, batch correction, integration, and perturbation prediction alongside its documented failure modes. Rice, maize, and wheat are compared to identify transferable methodology. Cell-resolved omics has to date improved biological interpretation and candidate prioritization; demonstrating an incremental breeding advantage from it remains an unmet requirement. Full article

(This article belongs to the Special Issue Latest Reviews in Molecular Plant Science 2025)

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28 pages, 8972 KB

Open AccessReview

Spatial Immune Coding in Tumor-Draining Lymph Nodes: Functional Compartmentalization of Immune Activation and Immunosuppression

by Jinjie Li, Wei Ping, Ruijie Zhang, Lin Peng, Yujie Zhang and Li Zhang

Int. J. Mol. Sci. 2026, 27(16), 7113; https://doi.org/10.3390/ijms27167113 (registering DOI) - 8 Aug 2026

Abstract

Tumor-draining lymph nodes (TDLNs) are important immune organs linking primary tumors with systemic immune responses. They support tumor antigen presentation, T-cell priming, and effector immune responses, but under sustained tumor influence they can also be remodeled into microenvironments that promote immune escape and [...] Read more.

Tumor-draining lymph nodes (TDLNs) are important immune organs linking primary tumors with systemic immune responses. They support tumor antigen presentation, T-cell priming, and effector immune responses, but under sustained tumor influence they can also be remodeled into microenvironments that promote immune escape and metastatic colonization. Conventional methods, including flow cytometry, bulk RNA sequencing, and routine immunohistochemistry, have advanced our understanding of TDLN immunity but cannot simultaneously preserve tissue architecture, cell identity, and spatial cell–cell relationships. Recent advances in spatial transcriptomics, spatial proteomics, and multiplexed imaging enable in situ analysis of immune cells, stromal cells, vascular structures, and their interactions within TDLNs. Emerging evidence suggests that TDLNs are not immunologically homogeneous organs, but gradually develop spatially distinct immune-activation and immunosuppressive regions during tumor progression. Activation regions are associated with HEV-mediated lymphocyte entry, DC–T-cell priming, B-cell follicles, and germinal-center reactions, whereas suppressive regions are enriched in Treg cells, exhausted T cells, suppressive myeloid cells, tumor-reprogrammed FRCs, and myeloid–CAF niches. This review summarizes spatial multi-omics studies of TDLN functional compartmentalization and discusses the potential value of TDLN spatial immune states in predicting immunotherapy response, assessing metastatic risk, and guiding precision treatment, thereby providing a reference for future spatial multi-omics studies of TDLNs. Full article

(This article belongs to the Special Issue Bioinformatics Analysis of Single Cell and Spatial Multi-Omics)

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15 pages, 940 KB

Open AccessReview

PSMA-Targeted Theranostics in Glioblastoma Multiforme: Current Evidence and Future Perspectives

by Francesca Russo, Maria Ricci, Habibollah Dadgar, Laura Travascio, Maria Silvia De Feo, Gabriele Brunotti, Sharjeel Usmani, Hossein Arabi, Farah M. Anwar, Aysar Najeh Khalaf, Luca Filippi and Andrea Cimini

Int. J. Mol. Sci. 2026, 27(16), 7112; https://doi.org/10.3390/ijms27167112 (registering DOI) - 8 Aug 2026

Abstract

Glioblastoma multiforme (GBM) is the most common brain tumor in the adult population, and it is characterized by poor prognosis; thus, new treatment strategies are strongly needed. Precision medicine is a rapidly growing field in oncology that identifies specific molecular features of tumor [...] Read more.

Glioblastoma multiforme (GBM) is the most common brain tumor in the adult population, and it is characterized by poor prognosis; thus, new treatment strategies are strongly needed. Precision medicine is a rapidly growing field in oncology that identifies specific molecular features of tumor cells and allows theranostic strategies (combining diagnosis and therapy). In nuclear medicine, prostate-specific membrane antigen (PSMA) represents an interesting molecular target in theranostics, considering its involvement in the neoangiogenesis of many kinds of tumors, including GBM. In this narrative review, we performed a web-based literature search to explore the current evidence regarding PSMA-targeted nuclear medicine theranostics in GBM, highlighting diagnostic applications, therapeutic potential, and future clinical perspectives. Full article

(This article belongs to the Special Issue Novel Diagnostic and Theragnostic Strategies in Brain Tumors)

34 pages, 5831 KB

Open AccessReview

Defined Natural Products as Adjunctive Therapies: Evidence-Gated Polypharmacology Across Molecular Targets, Human Exposure, Clinical Signals, and Safety Boundaries

by Yohan Seo and Joohan Woo

Int. J. Mol. Sci. 2026, 27(16), 7111; https://doi.org/10.3390/ijms27167111 (registering DOI) - 8 Aug 2026

Abstract

Defined natural products are often framed as intrinsically safer multi-target alternatives to selective drugs, but this assumption is not pharmacologically justified. This critical review evaluates product-specific adjunctive evidence in respiratory allergy, inflammatory bowel disease, type 2 diabetes, depression, and insomnia. MEDLINE/PubMed records published [...] Read more.

Defined natural products are often framed as intrinsically safer multi-target alternatives to selective drugs, but this assumption is not pharmacologically justified. This critical review evaluates product-specific adjunctive evidence in respiratory allergy, inflammatory bowel disease, type 2 diabetes, depression, and insomnia. MEDLINE/PubMed records published from 2020 to 23 June 2026 were prioritized, while earlier pivotal randomized trials and quantitative safety studies were retained. Evidence was gated by product identity, human exposure, exposure-compatible target engagement, incremental efficacy, and safety boundaries. Nigella sativa oil improved Asthma Control Test scores by 1.5 points over placebo after 4 weeks, although the clinical importance is uncertain and FEV1 was not significantly improved. Curcumin plus mesalamine induced remission in mild-to-moderate ulcerative colitis (53.8% versus 0%), whereas indigo naturalis produced strong response rates but is constrained by pulmonary arterial hypertension. Berberine improves glycemic surrogates but lacks cardiovascular or renal outcome evidence and shows commercial potency variability. Saffron has a short-term antidepressant signal, while St John’s wort combines extract-dependent efficacy with CYP3A4/P-glycoprotein induction. Overall, selected defined natural products may merit narrow adjunctive roles, but undefined mixtures should not be treated as mechanistically established interventions without batch-level characterization, human pharmacokinetics, objective endpoints, and prospective interaction surveillance. Full article

(This article belongs to the Special Issue The Structures, Syntheses of Natural Products, and Their Biological Effects)

24 pages, 4473 KB

Open AccessArticle

Artificial Intelligence-Guided Analysis of WNT Pathway Alterations: Associations with Genomic Burden and Survival Across African American and Non-Hispanic White Populations, Age Groups, and FOLFOX Treatment in Colorectal Cancer

by Tsion Zewdu Minas, Brigette Waldrup, Francisco G. Carranza, Sophia Manjarrez and Enrique Velazquez-Villarreal

Int. J. Mol. Sci. 2026, 27(16), 7110; https://doi.org/10.3390/ijms27167110 (registering DOI) - 8 Aug 2026

Abstract

Colorectal cancer (CRC) exhibits substantial heterogeneity across ancestry, age at onset, and treatment exposure. Although dysregulation of the WNT signaling pathway is a hallmark of CRC, its associations with genomic burden and survival across diverse clinical contexts remain incompletely understood. We analyzed 2562 [...] Read more.

Colorectal cancer (CRC) exhibits substantial heterogeneity across ancestry, age at onset, and treatment exposure. Although dysregulation of the WNT signaling pathway is a hallmark of CRC, its associations with genomic burden and survival across diverse clinical contexts remain incompletely understood. We analyzed 2562 CRC cases from AACR Project GENIE and cBioPortal, stratified by ancestry (African American [AA] and non-Hispanic White [NHW]), age at onset (early vs. late), and FOLFOX treatment status. Associations between WNT pathway alterations, genomic burden (mutation count, tumor mutational burden, and fraction of genome altered), and survival were assessed using conventional statistical methods. AI-HOPE and AI-HOPE-WNT conversational artificial intelligence platforms were used to facilitate data integration and exploratory analyses. WNT pathway alterations were highly prevalent across all subgroups and were predominantly driven by APC alterations. Late-onset CRC, particularly among NHW patients not treated with FOLFOX, exhibited higher mutation burden and enrichment of AXIN1 and AXIN2 alterations. Survival analyses demonstrated context-dependent associations between WNT alterations and outcomes. Among early-onset FOLFOX-treated patients, WNT alterations were associated with differential survival. In NHW patients, WNT alterations were linked to improved survival across multiple clinical settings, whereas associations in AA patients were more limited and context-specific. WNT pathway alterations are pervasive in CRC but exhibit ancestry-, age-, and treatment-dependent associations with genomic complexity and survival. AI-guided analyses may accelerate identification of clinically relevant subgroup-specific molecular patterns. Full article

(This article belongs to the Special Issue Colorectal Cancer: A Molecular Genetics Perspective (2nd Edition))

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23 pages, 27125 KB

Open AccessArticle

Shikonin-Loaded Nanoparticles Ameliorate DEHP-Exacerbated Psoriasis Skin Injury via Targeted Inhibition of the p38 MAPK Signaling Pathway

by Qinghua Tang, Yixiong Li, Yan Li, Xinyuan Wang, Yanan Bie, Xuesong Yu, Lin Zhou and Ming Li

Int. J. Mol. Sci. 2026, 27(16), 7109; https://doi.org/10.3390/ijms27167109 (registering DOI) - 8 Aug 2026

Abstract

Di-(2-ethylhexyl) phthalate (DEHP), a ubiquitous environmental plasticizer, has been increasingly linked to the exacerbation of inflammatory skin conditions, especially psoriasis. However, the mechanisms and effective therapeutic strategies targeting DEHP-aggravated psoriasis remain elusive. We integrated network toxicology, network pharmacology, and molecular docking to explore [...] Read more.

Di-(2-ethylhexyl) phthalate (DEHP), a ubiquitous environmental plasticizer, has been increasingly linked to the exacerbation of inflammatory skin conditions, especially psoriasis. However, the mechanisms and effective therapeutic strategies targeting DEHP-aggravated psoriasis remain elusive. We integrated network toxicology, network pharmacology, and molecular docking to explore the targets of DEHP-exacerbated psoriasis and the protective effects of shikonin (SH). These findings were validated in a DEHP/IMQ-induced mouse model using a novel shikonin nanoparticle (SH-NP) that overcomes SH’s inherent hydrophobicity. Computational analyses revealed that SH counteracts DEHP skin toxicity through a multi-target network, identifying the p38 mitogen-activated protein kinase (p38 MAPK), TNF, IL-1β, proliferating cell nuclear antigen (PCNA), and matrix metalloproteinases 2 and 9 (MMP2/9) as core therapeutic nodes. Molecular docking verified this network, revealing robust binding between SH and key targets with binding energies ranging from −6.0 to −7.8 kcal/mol, consistently outperforming DEHP. In vivo experiments demonstrated that topical application of SH-NP significantly ameliorated macroscopic skin injury and reduced PASI scores. Mechanistically, SH-NP effectively reversed the DEHP-exacerbated inflammatory microenvironment by decreasing macrophage and mast cell infiltration in the dermis, reducing pro-inflammatory cytokine levels, and inhibiting the phosphorylation of p38 MAPK. Furthermore, SH-NP treatment successfully suppressed keratinocyte hyperproliferation, as evidenced by downregulated PCNA expression and reduced epidermal thickness. SH-NPs also markedly downregulated the elevated levels of MMP2/9 in mice, thereby mitigating collagen degradation and maintaining dermal matrix integrity. This study shows that SH-NPs alleviate DEHP-aggravated psoriasis by suppressing local inflammation, keratinocyte hyperproliferation, and collagen degradation, offering a targeted nanostrategy for environmentally exacerbated skin diseases. Full article

(This article belongs to the Special Issue Psoriasis and Associated Complications: Pathogenic Mechanisms, Gene Biomarkers and Treatments)

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35 pages, 5667 KB

Open AccessReview

GLP-1 Receptor Agonists in Obstructive Sleep Apnea: A Translational Perspective on Mechanisms and Clinical Implications

by Isabella Gómez-Maldonado, Andrea Rodríguez-Arana, Alejandro Tamayo-Pinzón, Juan Esteban Albornoz-Suárez, María José López-Franco, Juan Andrés Mejia-Manrique, Juan Jacobo Forero-Caycedo, Luis Carlos Rojas-Rodríguez, Natalia Buitrago-Ricaurte, Mariana Gaviria-Carrillo, Jesús Rodríguez-Quintana and Carlos Alberto Calderón-Ospina

Int. J. Mol. Sci. 2026, 27(16), 7108; https://doi.org/10.3390/ijms27167108 (registering DOI) - 8 Aug 2026

Abstract

Obstructive sleep apnea (OSA) affects nearly one billion adults worldwide and involves mechanical upper-airway obstruction alongside metabolic dysfunction, systemic inflammation, and gut–brain axis disruption. Despite the efficacy of continuous positive airway pressure (CPAP), suboptimal long-term adherence highlights the need for complementary pharmacological strategies. [...] Read more.

Obstructive sleep apnea (OSA) affects nearly one billion adults worldwide and involves mechanical upper-airway obstruction alongside metabolic dysfunction, systemic inflammation, and gut–brain axis disruption. Despite the efficacy of continuous positive airway pressure (CPAP), suboptimal long-term adherence highlights the need for complementary pharmacological strategies. This narrative review synthesizes preclinical and clinical evidence on GLP-1-based therapies, encompassing selective GLP-1 receptor agonists and tirzepatide, a dual GIP/GLP-1 receptor agonist, in obesity-associated OSA. Preclinical studies show that GLP-1 receptor activation can reduce visceral adiposity, attenuate pro-inflammatory signaling, improve glucose and lipid metabolism, and modulate hypothalamic appetite circuits. However, the only identified murine study evaluating liraglutide during intermittent hypoxia—an experimental model of one component of OSA rather than the complete disorder—did not reverse hypoxia-induced insulin resistance, indicating that persistent intermittent hypoxia may limit metabolic improvement in that model. Clinically, liraglutide and tirzepatide have reduced the apnea–hypopnea index (AHI) and improved several cardiometabolic outcomes. Numerically larger AHI reductions were reported in the tirzepatide trials, although no head-to-head comparison with selective GLP-1 receptor agonists is available. Tirzepatide is approved by the U.S. Food and Drug Administration for moderate-to-severe OSA in adults with obesity, together with a reduced-calorie diet and increased physical activity, and may be used without concomitant positive airway pressure in eligible patients or as an adjunct to ongoing therapy. The observed respiratory benefits appear to be mediated predominantly by weight loss and related reductions in mechanical and metabolic burden. Evidence supporting additional weight-independent mechanisms remains insufficient, and longer-term mechanistic studies in broader populations are required. Full article

(This article belongs to the Special Issue Translational Pharmacology of GLP-1 Receptor Agonists Beyond Metabolic Diseases)

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