International Journal of Molecular Sciences doi: 10.3390/ijms27104353

Authors: Mila Taylor Michal Halicki Paul Chazot

Serving as central signalling organelles and hubs of metabolism, mitochondria are essential for cellular homeostasis. Mitochondrial disease can arise from mutations to nuclear or mitochondrial DNA, which result in disruptions to normal mitochondrial function. This generates a suite of rare disorders which are multi-system and often fatal. Variable tissue distribution of mitochondria, alongside a high degree of heterogeneity in associated phenotype, has resulted in an inadequate understanding and characterisation of mitochondrial disease. Addressing this issue is therefore crucial for better clinical management and patient outcomes. Cholesterol dyshomeostasis is a potential pathological hallmark of numerous mitochondrial diseases. Cholesterol is an essential lipid and bioactive compound involved in numerous mitochondrial and cellular processes. A growing number of studies have reported perturbations to cholesterol biosynthesis, cholesterol import, and cholesterol ratios in cell and animal models and individuals with mitochondrial disease, suggesting it could be a unifying feature of these disparate and variable disorders. This review summarises the current experimental evidence for the role of cholesterol dyshomeostasis in mitochondrial disease. It will further discuss reports of statin intolerance, generally attributed to off-target action on mitochondrial structures, in the context of this evidence. Ultimately, the necessity of further integrative clinical and experimental studies exploring the potential of cholesterol dyshomeostasis as a pathological hallmark of mitochondrial disease will be highlighted.

International Journal of Molecular Sciences doi: 10.3390/ijms27104352

Authors: Natasha B. Bambridge Yaoying Lu Horst Joachim Schirra Yunjiang Feng

The marine environment is an underutilised resource in probiotic research despite its potential for unique and beneficial microbes. Bacterial probionts derived from the ocean are emerging in the probiotic research field as an area of interest. Bacillus species (spp.) are Gram-positive, endospore-forming bacteria. Due to their unique resilience and their generally recognised as safe (GRAS) status, they have gained traction as putative probiotics. Existing large-scale reviews into the probiotic potential of Bacillus spp. have focused on terrestrial species, with limited attention given to marine-derived species. This review aims to address this gap by evaluating marine-derived Bacillus spp. with a focus on their diversity, origins, sources and demonstrated potential as probionts.

International Journal of Molecular Sciences doi: 10.3390/ijms27104351

Authors: Yonghui Bi Guanyu Zhang Yibing Wang Li Zhang Shuai Wu Yongqiang Zhang Xi Li Danfeng Yang

Constant light (LL) exposure is an established environmental risk factor for metabolic diseases, in which the whitening of brown adipose tissue (BAT) plays a critical role. This study aimed to elucidate the molecular mechanisms through which cordycepin counteracts LL-induced BAT whitening and improves metabolic function. We established an LL-exposed mouse model and employed an integrative approach combining pharmacological, metabolic, molecular, and computational (docking) assays to define cordycepin’s effects and targets. Cordycepin treatment significantly improved cold tolerance and attenuated BAT whitening in LL mice. Mechanistically, cordycepin directly bound to and enhanced the activity of the NAD+-dependent deacetylase SIRT1. This activation mitigated LL-induced impairments in mitochondrial biogenesis, dynamics, and autophagy. Furthermore, SIRT1 activation rebalanced fatty acid metabolism by downregulating CD36 and upregulating CPT1, thereby restoring the coupling of fatty acid uptake to oxidation. All beneficial effects of cordycepin were abolished by the selective SIRT1 inhibitor EX-527. In summary, our work provides strong evidence that cordycepin directly interacts with SIRT1 and enhances its deacetylase activity, thereby restoring mitochondrial function and fatty acid oxidative homeostasis in BAT to counteract constant LL-induced metabolic dysfunction. These findings position cordycepin as a promising natural compound targeting the SIRT1 pathway for metabolic disorders.

International Journal of Molecular Sciences doi: 10.3390/ijms27104347

Authors: Suli Shi Guozhi Yang Zhanggen Gu Qin Xue Yang Liu Lihua Ye

Anthocyanin biosynthesis in eggplant (Solanum melongena L.) is highly light-dependent, and insufficient light severely impairs fruit coloration, which restricts the development of the eggplant industry. SmMYB75 is a key positive regulator of anthocyanin biosynthesis, but its regulatory partners remain unclear. In this study, seven SmYABBY genes were identified from the eggplant genome, all containing conserved zinc finger and YABBY domains. Expression analysis showed that SmYABBY1 was predominantly expressed in fruit peel and significantly induced by light, with a peak at 4 h after light exposure. The yeast two-hybrid and bimolecular fluorescence complementation assays indicated that SmYABBY1 interacts with SmMYB75 and the light signaling regulator SmCOP1 in the nucleus. The heterologous overexpression of SmYABBY1 in Arabidopsis enhanced anthocyanin accumulation and upregulated the expression of anthocyanin structural genes. Transient co-expression in tobacco leaves further demonstrated that SmYABBY1 synergistically enhances SmMYB75-mediated anthocyanin biosynthesis. The yeast one-hybrid and Dual-LUC assays revealed that SmYABBY1 does not directly bind to the promoters of SmMYB75, SmDFR, and SmANS but indirectly promotes their transcriptional activity. Our results illustrate that SmYABBY1 acts as a transcriptional co-activator, interacting with SmMYB75 to promote anthocyanin accumulation, while SmCOP1 is involved in this regulatory process. This study provides a molecular basis for improving eggplant coloration under suboptimal light conditions.

International Journal of Molecular Sciences doi: 10.3390/ijms27104350

Authors: Velia Malizia Angela Marina Montalbano Anna Bonomolo Pietro Alfano Filippo Sapienza Ilaria Stanisci Stefania La Grutta Mirella Profita

Multiple interacting risk factors can influence the origin of asthma. Asthma is characterized by different clinical phenotypes, each of which includes different endotypes. There are four main clinical asthma phenotypes: (1) early-onset mild allergic asthma; (2) early-onset allergic moderate-to-severe remodeled asthma; (3) late-onset non-allergic eosinophilic asthma; and (4) late-onset non-eosinophilic non-allergic asthma. The main endotypes of asthma are T-helper (Th)-2 low and Th-2 high. The identification of asthma endotypes might help precision-based care move toward the personalized management of airway inflammation. In this scenario, it is important to know how the risk factors affect the pathophysiology of asthma. Accordingly, we focus our attention on the impact of obesity and air pollutants and how these risk factors together with epigenetic alterations influence the asthma phenotype/endotype and the pathogenesis of airway diseases. Our aim is to disseminate the progress of studies in this area by reporting recent observations on the topic. Finally, we believe that data/observations enclosed in this review suggest the need of further epidemiological studies to be useful to examine simultaneously the effect of more than one risk factor on clinical and biologic parameters of asthma.

International Journal of Molecular Sciences doi: 10.3390/ijms27104349

Authors: Sarfaraz K. Niazi

Artificial intelligence has advanced from merely predicting static protein structures to modeling equilibrium conformational ensembles. It now concurrently forecasts structure and binding affinity and actively participates in candidate selection during the initial stages of drug discovery. Foundation models introduced between 2024 and 2026, including BioEmu, AlphaFlow, DiG, Boltz-2, Chai-1, NeuralPLexer, and explicit-solvent prediction systems such as SuperWater, have begun to address issues previously identified as fundamental concerns in earlier critiques of AI in drug discovery. Nevertheless, many of these models are presently accessible only as preprints and require validation through independent peer review. Evidence indicates a shift in the primary bottleneck from representation challenges to validation difficulties. However, this transition remains incomplete and heavily dependent on context. The risks associated with AI-enabled drug discovery are increasingly not solely about the models’ capacity to accurately represent ensembles, but also about whether the evidentiary standards used to validate AI-derived predictions keep pace with the rapidity with which these predictions are generated and employed. This article introduces a four-tier validation framework designed to align the extent of computational and experimental evidence with the translational and regulatory risks associated with various artificial intelligence (AI) applications within the molecular sciences. These applications include machine learning (ML) models that analyze sequences, structures, conformational ensembles, protein–ligand complexes, and molecular dynamics trajectories. Tier 1 addresses the internal reproducibility of ML inference when applied to molecular inputs; Tier 2 pertains to the robustness of molecular-science benchmarks such as CASP, CASF-2016, PoseBusters, and OpenFE; Tier 3 involves prospective experimental validation against biophysical and biochemical measurements; and Tier 4 encompasses clinical and translational calibration within physiologically based pharmacokinetic (PBPK) and quantitative systems pharmacology (QSP) frameworks. This validation hierarchy functions as an explicit conceptual guide, serving as a framework rather than a regulatory requirement. It is firmly grounded in established principles derived from ICH Q8/Q9/Q10, the FDA model-informed drug development (MIDD) approach, the EMA reflection paper on AI in the medicinal product lifecycle, and the EU AI Act. The manuscript further incorporates recent evidence from ensemble-aware AI, prospective docking, free-energy campaigns, and clinical-stage AI-derived candidates. It concludes with specific recommendations pertaining to lifecycle governance, uncertainty reporting, and the adoption of harmonized evidentiary templates for AI/ML applications in the molecular sciences.

International Journal of Molecular Sciences doi: 10.3390/ijms27104348

Authors: Hyeonji Kim Ji-Woong Jeong Joo-Yun Kim Jae-Jung Shim Jae-Hwan Lee

Chronic kidney disease (CKD), a progressive disorder leading to renal dysfunction, remains a significant global health issue. This study investigated whether Lactiplantibacillus plantarum HY7718 modulates gut–kidney axis-associated inflammatory, gastrointestinal, and microbial alterations in a mouse model of adenine-induced chronic kidney disease. We examined fibrosis- and inflammation-related gene expression in mouse tissues and analyzed the gut microbiota via next-generation sequencing. HY7718 supplementation was associated with reduced expression of genes related to renal fibrosis (Col1a1, Acta2) and vascular inflammation (Icam-1, Vcam-1). Further, HY7718 suppressed intestinal inflammatory responses, including downregulation of pro-inflammatory cytokines (Tnf, Il-1β, Il-6) and TLR4/MyD88/NF-κB signaling pathway genes in the colon tissues. Gastrointestinal function was also improved, with significant upregulation of gastric motility-related genes and increased digestive enzyme activity. The gut microbiota composition was altered by HY7718, with reduced abundance of pro-inflammatory taxa such as Mucispirillum and Deferribacterota, whereas beneficial genera like Lactiplantibacillus were enriched. These microbial shifts were associated with reduced intestinal inflammatory and renal fibrosis-related markers. Overall, the findings indicate that HY7718 supplementation modulates gut–kidney axis-associated inflammatory, gastrointestinal, and microbial alterations in adenine-induced CKD mice and supports further investigation of this strain in CKD-related settings.

International Journal of Molecular Sciences doi: 10.3390/ijms27104346

Authors: Anton Ananev Karina Gilizhdinova Dinara Nurmieva Olga Yakovleva Kseniia Shaidullova Guzel Sitdikova

Migraines are a common neurological disorder that significantly reduces quality of life. The sensitization of trigeminal afferents is a key factor in the development of the pain syndrome associated with migraine. Carbon monoxide (CO) is produced endogenously by heme oxygenase (HO), widely expressed in structures involved in pain processing. In our study, the role of CO in an acute and chronic nitroglycerin (NTG)-induced rat migraine model was investigated using behavioral, electrophysiological, biochemical and histological methods. The repeated administration of a CO donor (CORM-2) or an HO-1 inducer (CoPP) decreased mechanical hypersensitivity and photophobia of rats in the NTG-induced migraine model. Additionally, CORM-2 and CoPP prevented an increase in trigeminal afferent excitability, which was evaluated by the frequency of action potentials in response to KCl application. Preliminary CORM-2 or CoPP injections promoted mast cell stability in the meninges and prevented NTG-induced CGRP elevation in blood plasma. Our results suggest that exogenously or endogenously produced CO has a protective potential in preventing inflammation and the sensitization of peripheral trigeminal afferents, the activity of which underlies the occurrence of pain in migraine. This could contribute to the development of new approaches for migraine prevention.

International Journal of Molecular Sciences doi: 10.3390/ijms27104340

Authors: Selena Wang Zahra Shafaei Pishabad Debina Sarkar Apeksha Arun Bhandarkar Makhdoom Sarwar Aaron Jeffs Glen Reid Antony Braithwaite Sunali Mehta

Y-box binding protein 1 (YB-1; encoded by YBX1) is a multifunctional DNA- and RNA-binding protein implicated in cell cycle regulation, DNA repair, stress adaptation, and therapy resistance. Elevated YBX1 expression has been associated with aggressive disease across multiple cancer types; however, its pan-cancer genomic and clinical correlates, and the extent to which these reflect proliferative activity versus genomic instability, remain incompletely defined. Here, we performed an integrative pan-cancer analysis across 53 independent datasets spanning 33 tumour types, incorporating transcriptomic (YBX1 mRNA), proteomic (RPPA), genomic, and clinical data. We found that YBX1 is rarely altered at the genomic level, whereas its mRNA expression is highly variable within tumour cohorts. Tumours with high YBX1 mRNA expression consistently exhibited conserved transcriptional programmes enriched for cell cycle, mitotic, RNA processing, and signalling pathways, patterns that were also reflected at the protein level by concordant pathway associations with elevated YB-1 abundance. These molecular features co-occurred with clinicopathological characteristics indicative of aggressive disease. High YBX1 mRNA expression was associated with increased mutation burden, chromosomal alteration burden, hypoxia, and homologous recombination deficiency at the pan-cancer level, with similar molecular associations observed in tumours stratified by elevated YB-1 protein levels. The association between YBX1 expression and chromosomal alteration burden was largely attenuated after accounting for proliferative activity, particularly G2/M-associated transcriptional programmes used as a proxy for mitotic activity. While the relationship with mutation burden was heterogeneous across tumour types, this pattern suggests that links between YBX1 expression and chromosomal instability primarily reflect shared proliferative and mitotic tumour biology rather than an independent genomic instability programme. Clinically, high YBX1 mRNA expression was associated with advanced disease stage, higher histologic grade, reduced progression-free survival, and poorer overall survival. Elevated YB-1 protein levels were also associated with advanced disease stage and poorer survival outcomes and demonstrated a similar, although non-significant, directional trend with histologic grade. Collectively, these findings demonstrate that elevated YBX1 expression marks proliferative and clinically aggressive tumour states within which genomic instability-related features arise in a context-dependent manner, providing a clarified pan-cancer framework for interpreting YB-1-associated tumour biology.

International Journal of Molecular Sciences doi: 10.3390/ijms27104345

Authors: Zakhiriddin Khojakulov Robin J. Palvadeau Müge Kovancılar-Koç Irmak Atay Irmak Şahbaz Şeyma Tekgül Ayça Şahin Esmer Zeynep Duru Badakal Tuğçe Gül-Demirkale Vildan Çiftçi Elif Bayraktar Ceren Tunca Natalia Smolina Fulya Akçimen Ayşe Nazlı Başak

Short tandem repeat (STR) expansions are a major cause of neurodegenerative disorders; however, their genetic and clinical heterogeneity complicates diagnosis. STR detection remains limited in routine short-read next-generation sequencing (NGS) workflows. We evaluated the diagnostic yield and clinical utility of computational STR genotyping in a large Turkish neurodegenerative disease cohort. ExpansionHunter was applied to NGS data from 3150 patients and 146 controls, targeting 15 disease-associated STR loci. To improve genotyping of poorly captured exonic regions in exome data, the default locus coverage threshold was reduced from 10× to 3×. Candidate expansions were visually inspected using REViewer and validated by conventional molecular methods. Computational analysis detected 28 pathogenic and 160 intermediate expansions. Of these, 23 were confirmed as pathogenic, and eight initially classified as intermediate were reclassified as pathogenic after conventional validation, resulting in 31 pathogenic cases across 28 families: HTT (n = 8), ATXN2 (n = 5), ATXN1 (n = 4), DMPK (n = 3), PABPN1 (n = 3), TBP (n = 2), and single cases in AR, ATN1, and CACNA1A. Lowering the coverage threshold markedly increased genotyping rates at low-coverage loci in exome data, particularly in ATXN2. Genetic findings were largely consistent with clinical pre-diagnosis and the additional diagnostic yield was 0.95%. These findings support integrating STR analysis into routine neurogenetic diagnostics.

International Journal of Molecular Sciences doi: 10.3390/ijms27104344

Authors: Virginie Freytag Veronika Butterweck Dominique J.-F. de de Quervain Georg Boonen Andreas Papassotiropoulos

Major depressive disorder (MDD) is associated with altered membrane lipids, but the causal species remain uncertain. Using two-sample Mendelian randomization (MR) on lipidomic GWAS data and the latest MDD meta-analysis (~400,000 cases; 1.5 million controls), we identified 49 lipid species linked to MDD risk, notably enriched for phosphatidylcholines. Protective lipids were enriched for long-chain polyunsaturated fatty acids (20:3–20:5), whereas shorter-chain or less unsaturated species, particularly 18:2-containing lipids, increased risk. These associations were also observed in a subset of clinically assessed MDD cases. Colocalization supported shared causal variants between many lipid traits and MDD, prominently at the FADS1/2 locus and additional loci, suggesting multiple entry points into lipid metabolism that differ partly from bipolar disorder. MR-implicated lipid shifts overlapped with cortisol-induced changes in a human cell stress model and were often reversed by co-treatment with St. John’s wort extract (Ze 117). Cholesteryl ester 20:3 emerged as a robust candidate marker, showing protective MR effects in two cohorts, colocalizing genetic support, normalization by Ze 117, and an inverse correlation with depressive symptom severity in a non-clinical sample. Together, these results define a depression-associated lipidomic signature centered on polyunsaturated fatty acid metabolism with biomarker and therapeutic potential.

International Journal of Molecular Sciences doi: 10.3390/ijms27104341

Authors: Aleksandra Ciechońska Mateusz Wierzbicki Barbara Nasiłowska Barbara Wójcik Wojciech Skrzeczanowski Katarzyna Ziółkowska Marta Kutwin

Pancreatic ductal adenocarcinoma (PDAC) is the most aggressive malignancy, characterized by rapid progression, early metastasis, and resistance to conventional therapies. Increasing evidence indicates that the behavior of residual tumor cells is strongly influenced by physicochemical properties of their microenvironment. Surface engineering strategies using nanostructured materials may therefore represent a complementary approach to modulating cancer cell activity. In this study, we investigated whether a graphene oxide (GO) aerosol nanofilm modifies the biological behavior of PDAC cells in vitro. The GO aerosol (4.5 g/L) was characterized using STEM, DLS, zeta potential measurements, LIBS, EDX, and FTIR spectroscopy. Ultrastructural analysis revealed thin, wrinkled GO sheets forming partially overlapping lamellar structures, while physicochemical characterization confirmed a highly oxidized stable nanomaterial. Human PDAC cell lines (BxPC-3 and AsPC-1) were cultured on GO-modified substrates to assess morphology (SEM), metabolic activity (XTT assay), migratory capacity (wound healing assay over 72 h), and expression of genes related to proliferation and epithelial–mesenchymal transition (EMT) by RT-qPCR. GO nanofilm significantly reduced cell viability and inhibited migration in both cell lines. SEM analysis demonstrated shortened cytoplasmic projections and altered membrane integrity. Gene expression profiling revealed cell line-dependent transcriptional responses, including modulation of components of the PI3K/AKT/mTOR pathway and EMT-associated markers. Collectively, our findings demonstrate that GO aerosol nanofilm alters PDAC cell morphology, viability, and migratory behavior in vitro. Surface-mediated modulation of tumor cell activity may represent a promising adjunct strategy for limiting residual cancer cell survival and metastatic potential.

International Journal of Molecular Sciences doi: 10.3390/ijms27104343

Authors: Vasiliki Venetsanaki Eleni C. Pardali Christos Cholevas Maria G. Grammatikopoulou Dimitrios G. Goulis Theoharis C. Theoharides

The global rise in cognitive decline and neurodegenerative disorders has intensified the search for safe and accessible strategies to support brain health. In recent years, nutraceuticals have gained considerable attention as potential modulators of neurological function due to their antioxidant, anti-inflammatory, and neuroprotective properties. Increasing evidence suggests that oxidative stress, neuroinflammation, mitochondrial dysfunction, and impaired neurovascular integrity play central roles in the pathogenesis of several neurodegenerative diseases, namely Alzheimer’s, Parkinson’s disease and autism spectrum disorder, among others. This narrative review provides an integrated overview of selected nutraceuticals with potential relevance to brain-related disorders, including biotin, folinic acid, flavonoids (apigenin, diosmin, luteolin, naringin, pycnogenol, and quercetin), huperzine A, Lion’s mane, olive oil polyphenols, oleuropein and palmitoylethanolamide. Rather than presenting a purely descriptive summary, we considered both mechanistic and clinical evidence, highlighting differences in the strength, consistency, and quality of available data across compounds. Among the reviewed compounds, huperzine A, specific flavonoids—particularly luteolin—and olive oil polyphenols demonstrated relatively stronger and more consistent support across experimental models and emerging clinical studies, mainly through modulation of cholinergic signaling, neuroinflammatory pathways, and oxidative stress responses. In contrast, evidence for other agents remains limited, heterogeneous, or primarily at the preclinical level. Overall, this review aims to provide a clearer and more structured synthesis of the current literature on neuronutrition, identifying compounds with the most promising profiles while outlining key limitations and research gaps that need to be addressed to better define their role in brain health.

International Journal of Molecular Sciences doi: 10.3390/ijms27104342

Authors: Krittakarn Udomkritayachai Theeraphat Thiamsuk Takdanai Jarujamrat Panaphas Kudikhong Sira Raksakhom Phitsamai Suphattana Natthanan Khankham Palapoom Thanawong Supakit Khacha-ananda

Cannabis-derived compounds are increasingly used as adjuncts in cancer therapy due to their reported antiproliferative and pro-apoptotic effects. However, potential drug–herb interactions with standard anticancer agents—namely sorafenib—remain unclear. This study investigated the interaction between cannabis and sorafenib, together with transcriptomic alterations in human hepatoma HepG2 cells. Cell viability was assessed using the MTT assay, and drug interactions were evaluated using the Combenefit program. RNA sequencing was performed to characterize gene expression changes across treatment groups. Combination analysis demonstrated concentration-dependent synergistic effects at intermediate doses. Transcriptomic profiling revealed that the combination treatment induced a broader and more distinct set of differentially expressed genes compared with single treatments. Integrated enrichment analyses showed consistent activation of stress- and inflammation-related pathways, including tumor necrosis factor-α via nuclear factor-kappaB (TNF/NF-κB), mitogen-activated protein kinase (MAPK), janus kinase/signal transducers and activators of transcription (JAK–STAT), oxidative stress, and p53-mediated apoptosis, alongside suppression of metabolic and proliferative processes. While several pathways were shared across treatments, the combination group exhibited a more coordinated transcriptional response, including enrichment of integrated stress response, cytokine signaling, endoplasmic reticulum stress, and epigenetic regulation. These findings were supported by increased reactive oxygen species production and apoptosis, particularly in the combination group. Overall, cannabis may potentiate sorafenib activity through enhanced cellular stress and anti-proliferative signaling.

International Journal of Molecular Sciences doi: 10.3390/ijms27104339

Authors: Nádia Ribeiro Melissa Albino Andreia Ferreira Cristina Escrevente Duarte C. Barral João Costa Pessoa Catarina Pinto Reis Maria Manuela Gaspar Isabel Correia

In the original publication [...]

International Journal of Molecular Sciences doi: 10.3390/ijms27104338

Authors: Emmy Drai Daniela Nahmias Blank Esther Hermano Adi Yifrach Ofer Chen Ofra Maimon Aron Popovtzer Tamar Peretz Amichay Meirovitz Michael Elkin

Obesity has been consistently associated with several types of malignant tumors, including hormone-responsive breast carcinoma (BC) in postmenopausal patients. BC is the most diagnosed malignancy and the leading cause of cancer-related morbidity and mortality among women worldwide. The predominant association between obesity and hormone-responsive BC subtypes is often explained by the increased local production of estrogens due to upregulation of aromatase, the rate-limiting enzyme in estrogen biosynthesis, in the chronically inflamed “obese” adipose tissue. However, the underlying molecular mechanisms are not fully defined. One potential mediator of inflammatory responses in the setting of obesity is bacterial endotoxin. Indeed, subclinical concentrations of endotoxin are chronically present in the circulation of obese patients and experimental animals (the phenomenon termed ‘metabolic endotoxemia’ [ME]). Here, we investigated whether ME conditions are mechanistically involved in augmented estrogen reactivity that sustains the obesity-BC link, focusing primarily on ME effects on key cellular components of the BC microenvironment (i.e., fibroblasts, macrophages). Our findings identify ME as a microenvironmental driver that directly induces aromatase expression in adipose fibroblasts, and simultaneously triggers upregulation of estrogen receptor levels in breast tumor cells via a macrophage-mediated mechanism. This dual action of ME in fueling obesity-accelerated hormone-dependent breast tumorigenesis may suggest new avenues for both therapeutic intervention and prevention of BC-promoting consequences of excess adiposity in an increasingly obese population.

International Journal of Molecular Sciences doi: 10.3390/ijms27104337

Authors: Pedro Maciel Caroline Barbalho Lamas Adriano Cressoni Araújo Eduardo F. B. Chagas Elen Landgraf Guiguer Rui Curi Tania Cristina Pithon-Curi Mariana Cristina da Silva Almeida Kátia C. Portero Sloam Lance A. Sloam Ana Luiza Decanini Miranda de Souza Claudio J. Rubira Claudemir G. Mendes Márcia Gabaldi Rocha Vitor E. Valenti Sandra M. Barbalho

Mitochondrial dysfunction is a key contributor to cognitive impairment, directly affecting neuronal viability, synaptic function, and energy metabolism. In the central nervous system, where energy demand is particularly high, disturbances in mitochondrial dynamics, including impaired oxidative phosphorylation (OxPhos), increased reactive oxygen species (ROS) production, and reduced ATP availability, can compromise synaptic transmission and accelerate cognitive decline. These alterations are commonly observed in neurodegenerative diseases such as Alzheimer’s (AD) and Parkinson’s (PD), in which mitochondrial dysfunction is closely associated with oxidative stress and neuroinflammatory processes. This review aims to investigate the role of mitochondrial dysfunction in cognitive impairment and the effects of physical exercise as a non-pharmacological strategy to mitigate these alterations. Current evidence indicates that exercise promotes mitochondrial biogenesis through activation of the AMPK/PGC-1α pathway, enhances oxidative metabolism, and improves mitochondrial efficiency. Furthermore, exercise reduces oxidative stress and inflammation while stimulating the release of neurotrophic factors, such as brain-derived neurotrophic factor which support neurogenesis, synaptic plasticity, and neuronal survival. Overall, these findings reinforce the importance of mitochondrial integrity in maintaining cognitive function and highlight physical exercise as a promising strategy to counteract mitochondrial dysfunction and delay the progression of neurodegenerative diseases.

International Journal of Molecular Sciences doi: 10.3390/ijms27104335

Authors: Daniel Alves dos Santos Guilherme Arthur Longhitano Gustavo Andrade Fraga Rogerio Leone Buchaim Daniela Vieira Buchaim João Paulo Mardegan Issa Vinicius Barroso Hirota Marina Ribeiro Paulini André Antonio Pelegrine Arnaldo Rodrigues Santos Rui Seabra Ferreira Junior Marcelo Rodrigues da Cunha

Treating fractures involving complex bone defects remains a major challenge in regenerative medicine. Additive manufacturing enables the fabrication of patient-specific implants, while surface anodization may enhance osseointegration by improving cell adhesion at the bone–implant interface. This study evaluated the feasibility of porous Ti-6Al-4V implants produced by additive manufacturing and surface-modified by anodization for repairing critical-sized femoral defects. Eighty rats were assigned to four groups: control (no graft), non-anodized Ti-6Al-4V implants, nanoporous implants, and nanotubular implants. After six weeks, bone regeneration and mechanical performance were assessed. Newly formed bone volume was significantly higher in the implanted groups compared to control (24.62 ± 3.11%), reaching 47.25 ± 3.92% (non-anodized), 58.20 ± 5.39% (nanoporous), and 40.72 ± 2.22% (nanotubular). Bone strength was also greater in implanted groups (150.27 ± 2.94 N, 151.98 ± 10.37 N, and 156.59 ± 4.95 N, respectively) compared to control (128.16 ± 2.17 N), with no significant differences among treated groups. No signs of implant rejection or inflammation were observed, indicating good biocompatibility. Anodized surfaces demonstrated enhanced osteogenic performance, particularly in the nanoporous group. These findings indicate that anodized porous Ti-6Al-4V implants produced by additive manufacturing combine biological compatibility with mechanical stability, supporting their potential application in bone reconstruction therapies.

International Journal of Molecular Sciences doi: 10.3390/ijms27104336

Authors: Irina Maltseva Aleksandr Yakoviichuk Svetlana Maltseva Maxim Kulikovskiy Yevhen Maltsev

This work described a novel freshwater strain of Cyanobacteria, Dolichospermum solitarium MAC–C17 from the Zaporozhye region in the south of European Russia and characterised its growth and biochemical parameters. The strain demonstrated high biomass, lipid, and protein productivity, comparable to the best-known data for high-productivity cyanobacteria. The highest protein content (383.76 mg g−1 dry weight) was in the exponential growth phase. In contrast, the highest content of lipids, vitamin E (α-tocopherol) and vitamin A (retinol) was in the stationary phase (150.05 mg g−1, 45.58 µg g−1 and 31.61 µg g−1). The productivity of Dolichospermum solitarium MAC–C17 was 19.26 mg L−1 d−1 for lipids, 42.54 mg L−1 d−1 for protein, 4.06 µg L−1 d−1 for retinol, and 5.85 µg L−1 d−1 for α-tocopherol. A distinctive feature of the new strain was its high chlorophyll a content (4.87–6.12 mg g−1). The antioxidant defence system of Dolichospermum solitarium differed between the exponential and stationary growth phases. During the exponential growth phase, strain MAC–C17 exhibited high catalase activity. In contrast, the stationary phase was characterised by a distinct shift in its antioxidant profile, marked by a substantial increase in superoxide dismutase and glutathione peroxidase activities, a significant rise in retinol and α-tocopherol levels. These findings suggest that strain Dolichospermum solitarium MAC–C17 possessed considerable biotechnological potential. It demonstrated strong potential as a producer of high-value commercial compounds, a promising candidate for developing antioxidant formulations, and a valuable asset for applications that boost agricultural yields and advance phytoremediation technologies.

International Journal of Molecular Sciences doi: 10.3390/ijms27104332

Authors: Pavel Navratil Minh Nguyet Tranova Adam Haluska Michal Lesko Igor Gunka David Astapenko

The endothelial glycocalyx (EG) is a dynamic endothelial surface layer composed of proteoglycans, glycosaminoglycans, glycoproteins, and adsorbed plasma proteins that regulates permeability, mechanotransduction, leukocyte trafficking, coagulation, and nitric oxide signaling. In kidney transplantation (KT), the EG is exposed to cumulative injury from recipient uremia, donor instability, preservation, machine perfusion, reperfusion, rejection, and immunosuppressive toxicity. This narrative review summarizes EG biology in KT, with emphasis on biomolecular findings relevant to ischemia–reperfusion injury, delayed graft function, rejection, and chronic allograft injury. Particular attention is given to syndecan-1, heparan sulfate, heparanase, soluble thrombomodulin, matrix metalloproteinases, angiopoietin-2/Tie2 signaling, selectins, miR-126, extracellular vesicles, and urinary or perfusate-derived readouts. Current evidence is biologically coherent but uneven: human data are largely observational, whereas many therapeutic concepts remain preclinical or exploratory. Glycocalyx-centered phenotyping may eventually improve risk stratification and trial enrichment, but clinical implementation will require standardized sampling, sample-source-aware biomarker panels, prospective validation, and clear separation between mechanistic plausibility and proven clinical utility.

International Journal of Molecular Sciences doi: 10.3390/ijms27104334

Authors: Ke Ying Xiang Zhao Zhuo Wu Chi Huang Qian Wu Zhongchen Liu

Colorectal cancer (CRC) progression is driven by dysregulated signaling networks that promote proliferation and metastasis. While SLC25A5 is a well-characterized mitochondrial ADP/ATP transporter, its potential non-canonical roles in cancer remain unclear. This study investigated whether SLC25A5 exerts tumor-suppressive functions in CRC. Using transcriptomic datasets and clinical cohorts, we found that SLC25A5 is significantly downregulated in CRC tissues, and low expression is associated with poor patient survival. Restoration of SLC25A5 suppressed CRC cell proliferation, epithelial–mesenchymal transition (EMT), and metastasis in vitro and in vivo. Mechanistically, co-immunoprecipitation and protein stability assays suggested an association between SLC25A5 and EIF3A and indicated that SLC25A5 may promote EIF3A destabilization through the ubiquitin–proteasome pathway without altering its mRNA levels. Subcellular fractionation further suggested the presence of a cytoplasmic pool of SLC25A5, providing a potential basis for this interaction. Rescue experiments showed that EIF3A overexpression partially reversed the tumor-suppressive effects of SLC25A5. In addition, SLC25A5 expression was associated with reduced PI3K/AKT signaling activity, and pharmacological activation of AKT partially restored invasive phenotypes. Collectively, these findings suggest an SLC25A5–EIF3A–PI3K/AKT regulatory axis and reveal a potential non-canonical role for this mitochondrial carrier in tumor progression. This study provides insight into how mitochondrial proteins may influence cytoplasmic signaling pathways in cancer.

International Journal of Molecular Sciences doi: 10.3390/ijms27104333

Authors: Alexandru Ionuț Neacșu Lucian-Ion Giubelan Bogdan Cătălin Alexandra Daniela Rotaru-Zăvăleanu Mădălina Iuliana Mușat Elena-Mădălina Neniu Alexandru Ionuț Irimie Daniel Pirici Eugen Osiac

Sepsis is a life-threatening syndrome driven by a dysregulated host response to infection and is frequently complicated by sepsis-associated encephalopathy (SAE), which contributes to long-term cognitive and neuropsychiatric sequelae. Despite advances in critical care, effective targeted therapies for SAE remain limited. Aquaporin-4 (AQP4), the predominant astrocytic water channel, plays a central role in cerebral water homeostasis, neuroinflammatory signaling, and blood–brain barrier integrity, suggesting its potential involvement in sepsis-induced cerebral dysfunction and neurorepair processes. Polymicrobial sepsis was induced in C57BL/6J mice using the cecal ligation and puncture (CLP) model. AQP4 activity was pharmacologically modulated through either inhibition or facilitation following sepsis induction. Disease severity was assessed using physiological parameters and a modified murine sepsis score. Neurological outcomes were evaluated through standardized behavioral tests assessing locomotor activity, motor coordination, cognitive performance, and depressive-like behavior. Neuroinflammatory and neuronal changes were examined by immunohistochemical analyses of microglial activation (Iba1), astroglial reactivity (GFAP), neuronal integrity (NeuN), and AQP4 expression. Compared with AQP4 facilitation, pharmacological inhibition of AQP4 was associated with a more favorable clinical recovery profile, reflected by lower sepsis severity scores and a more favorable body weight trajectory during the recovery phase. Behavioral analyses demonstrated preserved cognitive function, enhanced motor coordination, and reduced depressive-like behavior in AQP4 inhibitor-treated mice compared with animals receiving AQP4 facilitation. At the histological level, the inhibitor-treated group showed lower microglial and astroglial activation and better preservation of neuronal markers than the facilitator-treated group, whereas AQP4 facilitation exacerbated neuroinflammatory responses and neuronal alterations. These findings highlight a dual, context-dependent role of AQP4 in sepsis-associated cerebral dysfunction. These findings suggest that AQP4 modulation influences sepsis-associated cerebral dysfunction in a context-dependent manner. Within our experimental design, AQP4 facilitation was associated with worse outcomes, whereas AQP4 inhibition was associated with a comparatively more favorable neurobehavioral and histological profile.

International Journal of Molecular Sciences doi: 10.3390/ijms27104331

Authors: Eri Takayama Misaki Enomoto Manami Nagae Momoko Tomoda Yuta Miyazumi Yuki Iwaisako Ryota Shirasawa Youichi Suzuki Takashi Nakano Keiji Ueda Masahiro Fujimuro

Controlled delivery using nanoparticle-based systems has attracted considerable attention; however, achieving cell-type specificity remains a major challenge. To address this issue, we focused on the intrinsic cell tropism of viruses. The hepatocyte tropism of hepatitis B virus (HBV) is mediated by interactions between its large envelope protein (L protein) and host factors, including the sodium taurocholate cotransporting polypeptide (NTCP). In this study, we explored viral-like secretory vesicles (VLSVs) displaying HBV spike proteins as a virus-inspired vesicle platform for hepatocyte targeting. We previously established a method for producing VLSVs from HBV L- and S-expressing HEK293T cells. In the present study, we developed an improved protocol using exosome-depleted fetal calf serum and optimized ultracentrifugation, resulting in VLSVs with comparable particle numbers and sizes but approximately tenfold higher protein content per particle. VLSVs were concentrated using a two-layer sucrose cushion, labeled with DiI, and purified by sucrose density gradient ultracentrifugation. We evaluated DiI uptake in hepatocyte-derived cells (HepG2 and Huh7), non-hepatic cells (MDA-MB231, H1299, HeLa, and Vero), and NTCP-overexpressing HepG2 cells. VLSVs showed preferential uptake in the following order: NTCP-overexpressing HepG2 > HepG2 > Huh7 > non-hepatic cells. Furthermore, removal of the N-terminal Flag tag from the L protein enhanced hepatocyte-associated uptake, suggesting the importance of preserving the native structure of the preS1 domain. While vesicle characterization and mechanistic validation remain to be further investigated, these findings provide a proof-of-concept for a virus-inspired vesicle platform exhibiting preferential uptake in hepatocyte-derived cells.

International Journal of Molecular Sciences doi: 10.3390/ijms27104330

Authors: Kazuhiko Nakadate Nozomi Ito Kiyoharu Kawakami

Natural products have historically been integral to pharmacotherapy, attributed to their remarkable structural diversity and evolutionary refinement for biological interactions. Nonetheless, traditional natural product-based drug discovery has faced challenges such as mechanistic ambiguity, scalability limitations, and inadequate translational predictability. Concurrently, reductionist single-target approaches have been insufficient for addressing complex diseases characterized by network-level dysregulations. Recent advancements in analytical chemistry, genomics, and data-driven methodologies have rejuvenated natural product research by facilitating rapid structural elucidation, systematic exploration of biosynthetic diversity, and rational prioritization of bioactive compounds. Notably, many natural products exhibit multitarget effects that necessitate interpretation beyond isolated molecular interactions. Systems pharmacology offers a quantitative framework to analyze such network-level perturbations by integrating omics data, computational modeling, and experimental validation. However, molecular and computational predictions alone do not suffice to establish therapeutic relevance. Experimental pathology, encompassing histopathology, immunohistochemistry, spatial analysis, and ultrastructural evaluation, remains essential for validating efficacy and safety at tissue and organ levels. This review synthesizes technological innovation, systems pharmacology, and pathological validation to reposition natural products as mechanistically grounded and translationally robust resources for contemporary drug discovery.

International Journal of Molecular Sciences doi: 10.3390/ijms27104328

Authors: Bismarck Bernabe-Yepes Cecilia Zazueta

Succinate is a key intermediate of the Krebs cycle, which has increasing recognition for its roles beyond energy metabolism, including inflammation, cellular signaling, and metabolic regulation. Extracellular succinate, in particular, has been recognized as a signaling molecule that acts via the succinate receptor 1 (SUCNR1). SUCNR1-mediated signaling, however, demonstrates significant heterogeneity across various pathological contexts, resulting in varied and occasionally contradictory biological outcomes. This complexity underscores the context-dependent characteristics of succinate signaling and its significance in disease progression. This review will offer a comprehensive analysis of the signaling pathways activated during the interaction of succinate with its receptor in various tissues, as well as the potential of succinate regulation to ameliorate several pathological conditions.

International Journal of Molecular Sciences doi: 10.3390/ijms27104329

Authors: William Almaguer Melian Daymara Mercerón Martínez Briceida Bergado Acosta Jorge A. Bergado Rosado

Erythropoietin (EPO), the master regulator of erythropoiesis, is emerging as a pivotal mediator of brain repair. While its capacity to mitigate neural damage is well-documented, we posit that its most profound potential lies in actively orchestrating functional restoration. In the present review we summarize the molecular biology of EPO and the evidence establishing EPO as a potent modulator of neuroplasticity. We use an experimental strategy in which a specific behavioral task marks experience-activated neural circuits, and a subsequent, temporally precise administration of EPO provides a surge of plasticity-related proteins. This creates a synergistic interaction where the proteins are selectively captured by the activated synapses, directing plastic changes with high specificity. We present experimental evidence demonstrating that this synchronized protocol enables the recovery of spatial memory, reinstates synaptic plasticity, and activates genetic programs for plasticity in rodent models of brain injury. Furthermore, we show that endogenous EPO signaling is itself activity-dependent and integral to memory formation. This redefines EPO as a precision tool for neurorestoration, a potential now being pursued with engineered, non-erythropoietic variants of EPO in clinical trials for neurological and psychiatric disorders.

International Journal of Molecular Sciences doi: 10.3390/ijms27104327

Authors: Feryal H. Alharthy Jawaher Alsughayyir Mohammad A. Alfhili

Omega-6 polyunsaturated fats (ω-6 PUFAs) are vital for many physiological functions, but their impact on cardiovascular disease (CVD) risk is controversial. Eryptosis alters blood viscosity by providing a procoagulant surface and leads to anemia, which is a recognized risk factor for CVD. This study examines the toxic mechanisms of adrenic acid (ADR), an ω-6 PUFA enriched in inflammatory and oxidative conditions, in red blood cells (RBCs). Purified RBCs were prepared from healthy volunteers and treated with 10–100 μM of ADR for 24 h at 37 °C under various physiological conditions. Eryptotic markers were studied through flow cytometry including Ca2+ (Fluo4/AM), loss of volume (forward scatter), phosphatidylserine (PS) exposure (annexin-V-FITC), and oxidative stress (H2DCFDA). Moreover, hemolytic markers were measured by colorimetric methods, whereas cellular morphology was visualized using a scanning electron microscope. ADR led to significant Ca2+ elevation, cell shrinkage and schistocyte formation, PS externalization, hemolysis, and oxidative stress. While guanosine, heparin, and NSC 23766 prevented eryptosis and hemolysis, melatonin, ATP, adenine, and L-NAME only prevented eryptosis. Conversely, mannitol and urea exacerbated eryptosis, whereas caffeine, mannitol, and urea under Ca2+ deprivation and membrane potential dissipation aggravated hemolysis. ADR induces erythrocyte membrane injury and eryptosis through Ca2+ elevation, oxidative stress, and metabolic exhaustion subject to inhibition by the Rac1 GTPase/NOS/COX pathway. Altogether, these findings present a novel mechanistic link between lipid dysregulation and RBC dysfunction which may improve dietary strategies to prevent and manage CVD.

International Journal of Molecular Sciences doi: 10.3390/ijms27104326

Authors: Chrysilla Espy Vaz Manasa Suresh Leona Dcunha Rajesh Raju Saptami Kanekar

Caveolin-1 (CAV1) is a 21 kDa Vesicular Integral-membrane Protein essential for the biogenesis of caveolae, invaginations of the plasma membrane that coordinate membrane trafficking, lipid homeostasis, and signal transduction. CAV1 functions as a scaffolding platform that integrates mechanotransduction, endocytosis, and cellular stress responses, thereby modulating vascular integrity, inflammation, metabolism, and tumorigenesis. To comprehensively understand the phosphorylation landscape of CAV1, global phosphoproteomic datasets and their corresponding experimental metadata were systematically curated and integrated from previously published human cellular studies. The phosphorylation sites with the highest detection frequency across these datasets were considered predominant phosphorylation sites. To assess their functional relevance, phosphosites in other proteins (PsOPs) co-regulated with the predominant CAV1 sites, along with their upstream kinases and high-confidence protein–protein interaction partners, were systematically analyzed. Analysis of global human cellular phosphoproteome datasets revealed that tyrosine 14 (Y14) and serine 37 (S37) of CAV1 are the most frequently detected phosphosites across diverse experimental conditions. Notably, many of the co-regulated proteins obtained were associated with carcinogenesis, apoptosis, and cell cycle regulation, including MET and ERBB2. Our analysis revealed SRC, ABL2, ERBB2, ERBB3, LYN, and TEC as potential upstream kinases of CAV1_Y14, whereas CSNK1E and GRK5 were predicted to regulate CAV1_S37. Considering the challenges associated with site-specific interrogation, we employed a global co-regulation analysis approach to characterize CAV1 phosphorylation dynamics. Our findings reveal that key CAV1 phosphosites modulate oncogenic signaling, cytoskeletal remodeling, and membrane organization, providing novel insights into CAV1-mediated cellular functions and its context-dependent role in tumor progression.

International Journal of Molecular Sciences doi: 10.3390/ijms27104325

Authors: Wiebke Schulten Nele Johanne Czaniera Mehran Fazel Barbara Kaltschmidt Christian Kaltschmidt

The APOE4 allele represents the strongest genetic risk factor for late-onset Alzheimer’s disease (AD), yet its influence on early cellular programs remains poorly understood. In this study, we investigated transcriptional differences between human induced pluripotent stem cells (iPSCs) carrying the APOE3 or APOE4 genotype. RNA sequencing revealed pronounced genotype-dependent transcriptional changes, with enrichment of genes associated with neural development and metallothioneins in APOE4 cells, while genes related to extracellular matrix organization and cell adhesion were downregulated. Protein–protein interaction network analysis confirmed the presence of clusters linked to neurodevelopmental processes and cellular stress responses in APOE4 cells. Increased expression and nuclear localization of the early neural marker SOX1 further suggest a shift towards early neural lineage commitment in APOE4 cells. In addition, altered expression of early growth response (EGR) transcription factors and reduced TNFR2 protein levels indicated genotype-specific differences in stress and inflammatory signaling pathways. Together, these findings suggest that APOE genotype-dependent alterations in transcriptional regulation, stress responses, and inflammatory signaling may already emerge in pluripotent cells and potentially influence early differentiation programs.

International Journal of Molecular Sciences doi: 10.3390/ijms27104324

Authors: Gaetana Gambino Gemma Marcelli Paola Iacopetti Laura Benvenuti Chiara Bertini Lucia Giambastiani Luisa Pozzo Alessandra Salvetti Leonardo Rossi

Natural products remain a major source of anticancer agents, yet freshwater organisms are largely unexplored. Building on our previous evidence that planarian mucus exerts cytostatic and cytotoxic effects on cancer cells, we investigated the involvement of endoplasmic reticulum stress and unfolded protein response (UPR) pathways. Mucus-induced cytotoxicity is ROS-dependent and associated with depletion of intracellular reduced glutathione (GSH), not through inhibition of the System Xc− transporter but potentially associated with upregulation of CHAC1, a glutathione-degrading enzyme. Mucus fractionation based on molecular weight identified the high-molecular-weight crude fraction as the one containing the bioactive entity, reproducing the effects of whole mucus. Treatment with this fraction early activates the PERK–ATF4 branch of the UPR, which could be responsible for driving CHAC1 induction. Moreover, ATF4 enhances DDIT3 expression, and activates a compensatory NRF2-dependent antioxidant response. At a later stage mucus also activates the IRE1α–XBP1 axis, with no ATF6 involvement, indicating selective UPR engagement in response to oxidative and lipid stress. Overall, our data are consistent with a potential PERK–ATF4–CHAC1–GSH self-sustaining axis promoting oxidative stress that culminates in cell death, supporting the potential of planarian mucus as a source of pleiotropic bioactive compounds, although the molecular identity of the active component(s) remains still unresolved.

International Journal of Molecular Sciences doi: 10.3390/ijms27104323

Authors: Aliya Orassay Naizabek Yerzhigit Anastassiya Ganina Elmira Chuvakova Oleg Lookin Abay Baigenzhin

Traditional treatments of autoimmune diseases relying on systemic immunosuppression often lack curative potential and have severe side effects. Mesenchymal stem cells (MSCs) are a promising alternative due to their immunomodulatory properties; however, whole-cell therapies have certain limitations. MSC-derived extracellular vesicles (EVs), including small vesicles—exosomes—have emerged as a safe cell-free therapeutic platform capable of crossing biological barriers and delivering bioactive cargo with low immunogenicity. Various types of RNAs abundantly produced by host MSCs represent a key element of EV content. In particular, EVs carry small RNAs, which essentially determine cellular life and fate. Our review provides a comprehensive mechanistic framework for the use of RNA-loaded EVs, specifically those carrying microRNAs (miRNAs), small interfering RNAs (siRNAs), and messenger RNAs (mRNAs), in restoring immune homeostasis. We detail the biogenesis and molecular mechanisms governing sorting of RNA into EVs, along with endogenous and exogenous engineering strategies to enhance therapeutic potency. We examine how RNA-loaded EVs modulate immunological processes like reprogramming of macrophage M1-M2 polarization, Th17/Treg balance, and suppression of inflammatory signaling pathways such as NF-κB and the NLRP3 inflammasome. We address critical translational challenges—EV heterogeneity, manufacturing scalability, and need for standardized quality control—while outlining future opportunities for RNA-loaded EV-based therapeutics.

International Journal of Molecular Sciences doi: 10.3390/ijms27104321

Authors: Itzchak Angel Kalaichitra Periyasamy Benin Joseph Erez Aminov

Obesity resulting from melanocortin-4 receptor (MC4R) dysfunction is characterized by combined metabolic dysregulation and maladaptive reward-related behaviors that limit the durability of existing therapies. The endocannabinoid system is a central regulator of appetite, lipid metabolism, and reward processing; however, first-generation cannabinoid receptor 1 (CB1) antagonists were limited by adverse neuropsychiatric effects. SKNY-1 is an orally active tetrahydrocannabivarin (THCV) analog designed to engage pathway-biased CB1 signaling, modulate cannabinoid receptor 2 (CB2), and selectively inhibit monoamine oxidase B (MAO-B), with the objective of addressing both metabolic and behavioral components of obesity while minimizing central nervous system liability through biased CB1 signaling, CB2 modulation, and potential complementary MAO-B inhibition. Here, we integrated in vitro pharmacological profiling of SKNY-1 with in vivo evaluation in an adult mc4r(G894C) zebrafish model exhibiting obesity-associated metabolic and reward-related phenotypes. In vitro, SKNY-1 displayed low-potency modulation of CB1 cyclic AMP signaling (EC50 ~30 µM) but more potent antagonism of the CB1 β-arrestin pathway (IC50 ~6 µM), consistent with differential CB1 pathway modulation. SKNY-1 acted as a CB2 partial agonist (EC50 ~0.1 µM), with antagonist activity emerging at higher concentrations, and selectively inhibited MAO-B at low affinity with no activity against MAO-A. In vivo, mc4r(G894C) zebrafish mutants exhibited dyslipidemia, hepatic triglyceride accumulation, altered appetite-regulatory gene expression, increased metabolic rate, and enhanced compulsive high-calorie feeding and nicotine-seeking behaviors. Oral administration of SKNY-1 for six days produced dose-dependent effects. Both doses normalized total cholesterol and low-density lipoprotein levels and reduced hepatic triglycerides toward wild-type values without affecting circulating triglycerides. The higher dose (200 ng per fish per day) induced significant body weight reduction while preserving body density and attenuated reward-associated feeding and nicotine-seeking behaviors. The lower dose (20 ng per fish per day) more effectively normalized the leptin a-to-ghrelin expression ratio. Collectively, these findings demonstrate that SKNY-1 engages integrated endocannabinoid and potential dopaminergic mechanisms to improve metabolic parameters and attenuate maladaptive reward-related behaviors in an MC4R-deficient vertebrate model, supporting its further translational investigation for obesity complicated by compulsive eating and substance-seeking behaviors.

International Journal of Molecular Sciences doi: 10.3390/ijms27104322

Authors: Fuhan Jiang Bowen Dong Yijue Wang Yi Xiong

The progressive decline in immune function during aging, termed immunosenescence, is increasingly recognized as a critical driver of skeletal fragility and impaired bone regeneration. This age-associated phenomenon—driven by thymic involution, inflammaging, and the accumulation of senescent immune cells—disrupts bone homeostasis primarily through the establishment of a pro-inflammatory milieu, wherein senescence-associated secretory phenotype (SASP) factors directly reprogram the function and fate of mesenchymal stem cells, osteoblasts, osteoclasts, and chondrocytes. Clinically, this immune-driven disruption of the bone microenvironment manifests across a spectrum of age-related skeletal disorders—including osteoporosis and osteoarthritis as prototypes of systemic and local bone loss, respectively, as well as delayed fracture healing, intervertebral disc degeneration, and periodontitis as paradigms of impaired regenerative and defensive responses. Despite advances in osteoimmunology revealing bidirectional immune-bone interactions, the mechanistic links between senescent immune cells and bone pathophysiology remain incompletely defined, presenting a significant barrier to therapeutic innovation. Herein, we synthesize current evidence to elucidate how immunosenescence, through the dysfunction of both innate and adaptive immunity, progressively dismantles bone homeostasis. We critically evaluate current challenges in dissecting the relative contributions of immunological memory accumulation versus fundamental aging processes to skeletal decline. We identify key knowledge gaps and propose strategic research directions, including longitudinal human immunophenotyping studies and innovative organoid-immune aging models. Such approaches hold the potential to transform the therapeutic landscape of age-related skeletal diseases by enabling precision interventions that target specific immunosenescence pathways to rejuvenate the aging skeleton.

International Journal of Molecular Sciences doi: 10.3390/ijms27104320

Authors: John S. Hingle Rhys S. McColl Ivan J. Vechetti Kathryn H. Myburgh

The skeletal muscle (SkM) secretome has been widely studied since the establishment of its endocrine function. Extracellular vesicles (EVs) are the most recently identified elements of the SkM secretome. These nano-sized lipid-bound vesicles carry molecular cargo and function as a means of intercellular communication. The effect of exercise on SkM EV micro-RNA cargo (miRNAs) remains a challenge to elucidate. Electrical pulse stimulation (EPS) was applied to C2C12 myotubes at high (30 Hz) and low (2 Hz) frequencies. EVs released during 10 h of stimulation were isolated and characterized and used to treat myoblasts. Their miRNA cargo was sequenced. EVs were used to treat myoblasts (2.19 × 108 EVs per mL) to determine the effects on myoblast migration and differentiation. Sequencing revealed over 300 known miRNAs packaged into myotube EVs. Many were differentially expressed after EPS, either positively or negatively. Muscle-important miRNAs were present (miR-206 was 4.8-fold more prevalent than any other miRNA). EV treatments improved myoblast migration and differentiation without a frequency-specific influence. Gene Ontology analysis based on differentially expressed miRNAs between control and EPS-EVs indicates an effect of EPS frequency on muscle EV signaling.

International Journal of Molecular Sciences doi: 10.3390/ijms27104318

Authors: Noreen Begum Shumaila Noreen Farhad Badshah Ahmed Mahmoud Ismail Manal Hadi Ghaffoori Kanaan Irfan Ullah Ahmed Othman Alsabih Saeedah Almutairi Aljawharah Fahad Alabbad Mostafa A. Abdel-Maksoud Syeda Kubra Hamid Ur Rahman

Monacha cartusiana (O. F. Müller, 1774), native to the Mediterranean region and Europe, is a terrestrial gastropod recognized as a highly destructive agricultural pest that causes significant damage to crop plants, fruit trees, vegetables, ornamentals, and natural ecosystems. Despite its broad geographic distribution, the evolutionary history and phylogeographic relationships of M. cartusiana populations remain globally unexplored. This study reports the first molecularly confirmed record of M. cartusiana in Pakistan and investigates its genetic diversity and phylogeographic structure within a global context using mitochondrial markers. After morphological identification, genomic DNA was extracted from collected specimens using the CTAB method, followed by amplification and sequencing of the mitochondrial COI and 16S rRNA genes. The resulting sequences were subsequently analyzed using DnaSP and PopART software to estimate genetic diversity, perform neutrality tests, and construct haplotype networks. Published sequences of M. cartusiana retrieved from GenBank were incorporated to provide a global comparative framework. The COI dataset (555 bp) revealed 52 haplotypes, whereas the 16S rRNA dataset (269 bp) identified 14 haplotypes across global populations. High haplotype diversity (Hd = 0.946 for COI; Hd = 0.831 for 16S rRNA) and moderate nucleotide diversity (π = 0.010 for COI; π = 0.01253 for 16S rRNA) indicated substantial genetic variability within the species. Neutrality tests produced negative and insignificant values for Tajima’s D for COI and significant values for 16S rRNA (−1.428 for COI; −0.20586 for 16S rRNA) and Fu’s Fs (−29.776 for COI; −1.263 for 16S rRNA), suggesting historical population expansion. Phylogenetic reconstruction and haplotype network analyses identified two major clades (Clade A and Clade B), reflecting genetic relationships among populations from different geographic regions. AMOVA based on COI and 16S rRNA sequences revealed significant population structuring, with 29.98–51.30% of the total genetic variation occurring among populations and high fixation indices (FST = 0.299–0.51398, p = 0.001), indicating pronounced genetic differentiation and restricted gene flow. Pairwise FST analyses indicated that the Pakistani population is most closely related to populations from Italy and Central Europe, suggesting a closer genetic affinity with Southern or Central European populations. However, FST alone does not allow definitive inference of introduction directionality, and additional analyses would be required to robustly identify the source population. Overall, this study provides the first comprehensive molecular and phylogeographic assessment of the M. cartusiana species from Pakistan within a global context. These findings contribute important baseline data for understanding the evolutionary dynamics, dispersal history, and population connectivity of this economically important pest species. The pronounced genetic differentiation among populations and the suggested genetic affinity of the Pakistani population with European lineages have direct implications for biosecurity monitoring, invasion pathway tracing, and targeted pest management strategies. Future research integrating nuclear markers with the mitochondrial data presented here will be essential for a more complete understanding of gene flow and local adaptation in this species.

International Journal of Molecular Sciences doi: 10.3390/ijms27104319

Authors: Carlo F. Medina-Ramírez Jose L. Chavelas-Reyes Josefina G. Rodríguez-González Nadia A. Fernández-Santos Lihua Wei Francisco J. Cabrera-Santos Eli J. Fuentes-Chávez Luis M. Rodríguez-Martínez Mario A. Rodríguez Pérez

Understanding the molecular mechanisms underlying host immune responses to SARS-CoV-2 vaccination remains essential, particularly in populations with a high prevalence of obesity. In this cross-sectional study, we evaluated whether body mass index (BMI) is associated with vaccine-induced humoral immunity in a cohort from northeastern Mexico and discuss the findings within a structural immunology framework of spike antigenicity and antibody–epitope interactions. A total of 138 adults were recruited in Reynosa and Matamoros (June 2021–June 2022) and categorized as healthy weight, overweight, or obese according to BMI criteria. Serum anti-SARS-CoV-2 IgG was assessed using an ELISA-based assay, and differences across BMI groups were tested using the Kruskal–Wallis approach. Among all participants, 33.3% were classified as obese and 99.3% (137/138) were seropositive for anti-SARS-CoV-2 IgG. No significant differences in IgG levels were detected between BMI categories (p = 0.20). These results indicate that, in this Mexican cohort—sampled during a period of heterogeneous and often incomplete vaccination schedules—obesity was not associated with reduced detectable anti-SARS-CoV-2 IgG responses. Our findings support the need to integrate population-level serology with mechanistic studies that interrogate antibody quality (e.g., neutralization potency and epitope specificity) to better connect clinical determinants such as obesity with molecular correlates of protection.

International Journal of Molecular Sciences doi: 10.3390/ijms27104317

Authors: Xinyi Cheng Yu Cai Yiran Geng Xiaoying Zang Jia Liu Qingxian Luan

Periodontitis is a chronic inflammatory disease remaining elusive with its pathogenesis. Mitochondrial dysfunction and aberrant immune activation are implicated, but the underlying mechanisms remain incompletely understood. Given the essential role of Ca2+ homeostasis in maintaining normal mitochondrial function, we investigated the role of mitochondrial calcium (mtCa2+) dysregulation in periodontitis. Gingival tissues from periodontitis patients and healthy controls, as well as cultured gingival fibroblasts stimulated with Porphyromonas gingivalis lipopolysaccharide, were examined using transmission electron microscopy, confocal imaging, flow cytometry, qPCR, and western blotting. Notably, mtCa2+ was overloaded under inflammatory conditions, accompanied by disruption of whole-cell Ca2+ homeostasis. We also observed marked mitochondrial ultrastructural damage, mitochondrial DNA (mtDNA) leakage, and activation of the cyclic GMP-AMP synthase (cGAS)- stimulator of interferon genes (STING) pathway. The mitochondrial Ca2+ channel proteins, voltage dependent anion channel 1 (VDAC1) and mitochondrial calcium uniporter (MCU), were significantly upregulated in periodontitis gingiva, and their expression positively correlated with probing depth. Pharmacological inhibition of VDAC1 or MCU attenuated mtCa2+ overload, reduced mtDNA release and downregulated pro-inflammatory cytokines. These findings link mtCa2+ overload to mtDNA leakage and innate immune activation in periodontitis, and identify VDAC1 and MCU as promising therapeutic targets to restore mtCa2+ homeostasis and control host immune responses.

International Journal of Molecular Sciences doi: 10.3390/ijms27104316

Authors: Polina A. Golubinskaya Evgenii S. Ruchko Alexandra N. Bogomazova Artem V. Eremeev

Most high-tech drugs and tissue engineering products based on human chondrocytes currently available on the market are aimed at restoring traumatic damage to cartilage tissue. However, in the presence of inflammation, their regenerative potential is significantly reduced, which limits their use in patients with osteoarthritis—one of the most common degenerative and inflammatory joint pathologies. The central element of the pathogenesis of osteoarthritis is inflammation—not classical acute inflammation, but rather chronic low-grade inflammation, primarily mediated by mechanisms of the innate immune response. Therefore, a key challenge is to enhance the anti-inflammatory effectiveness of cell-based drugs to broaden their indications to include degenerative diseases such as osteoarthritis and arthrosis. In recent years, cell-based drugs using stem cells, including mesenchymal stem cells (MSCs), hematopoietic stem cells (HSCs), and stromal vascular fraction (SVF) cells, have been actively studied. Despite their confirmed safety in inflammatory processes, meta-analyses of clinical trials show limited effectiveness in improving symptoms and MRI data in the treatment of osteoarthritis. A promising direction appears to be the development of combined cell-based drugs that combine MSCs with M2-polarized macrophages; however, data on their clinical effectiveness are still insufficient. This review explores key cellular effectors of inflammation and its molecular mechanisms, potential strategies for creating tissue engineering products that possess not only regenerative but also pronounced anti-inflammatory effects. The development of such products will expand their application in the treatment of inflammatory-degenerative joint diseases.

International Journal of Molecular Sciences doi: 10.3390/ijms27104310

Authors: Xuan Liu Yuqing Ding Tao Chen Zhengkang Wu Shujuan Hu Xianwang Wang

This study explored the regulatory role of nuclear factor E2-related factor 2 (Nrf2) in aerobic exercise improving oxidative stress and inflammatory responses in mice with insulin resistance (IR) induced by a high-fat diet. We established an IR mouse model through a high-fat diet, then subjected the IR mice to aerobic exercise, intraperitoneal injection of luteolin, or a combined intervention. After 6 weeks of intervention, we measured serum lipid and glucose profiles; evaluated skeletal muscle morphology by H&E staining; quantified mRNA expression levels of Nrf2 and its downstream targets in the skeletal muscle by RT-qPCR; and determined protein abundance, localization, and expression patterns of Nrf2 and NOD-like receptor protein 3 (NLRP3) inflammasome by Western blotting and immunohistochemistry, respectively. In the skeletal muscle of IR mice, Nrf2 and its downstream targets were significantly down-regulated, whereas NLRP3 inflammasome was markedly up-regulated (p < 0.05 or p < 0.01). IR mice subjected to aerobic exercise exhibited reduced serum glucose and lipid levels together with a lower insulin-resistance index (p < 0.05 or p < 0.01); morphologically, inter-myofibrillar spaces were narrowed, intrafiber vacuoles diminished, and cellular integrity restored. Concomitantly, Nrf2 and its downstream targets were up-regulated, whereas NLRP3 inflammasome components were down-regulated in the skeletal muscle (p < 0.05 or p < 0.01). Intraperitoneal administration of luteolin during exercise, however, partially attenuated or reversed these exercise-induced improvements by inhibiting the activation of Nrf2 (p < 0.05 or p < 0.01). These results indicate that aerobic exercise confers protective effects against IR by activating the Nrf2 signaling pathway, thereby attenuating oxidative stress and inflammation; these benefits are markedly attenuated when Nrf2 activity is pharmacologically inhibited.

International Journal of Molecular Sciences doi: 10.3390/ijms27104315

Authors: Muzi Li Renhou Jia Rong Huang Jiamin Wang Zilin Qiao Na Sun

Vero cells in high-density vaccine cultures often face nutrient starvation, especially in suspension-adapted Vero cells. Previous studies showed that serum starvation dramatically enhances autophagy and mitophagy in suspension-adapted Vero cells. Transcriptomic profiling also revealed significant upregulation of DDIT3, a marker of endoplasmic reticulum stress (ERS), in suspension-adapted Vero cells compared to adherent cells. To investigate the functional role of DDIT3, an Earle’s Balanced Salt Solution (EBSS)-induced starvation model was established in adherent Vero cells, recapitulating key autophagy and ER stress responses observed under suspension conditions. The genetic silencing of DDIT3 by shRNA attenuated autophagy, as evidenced by a reduced LC3-II/LC3-I ratio and impaired autophagosome–lysosome activity. Notably, DDIT3 knockdown enhanced cell proliferation and increased the yield of H1N1 influenza virus under nutrient-deprived conditions. Collectively, these results suggest that DDIT3 may serve as a critical regulator linking ER stress to autophagy in Vero cells, and that the suppression of DDIT3 may represent a promising strategy for developing autophagy-resistant Vero cell lines suitable for high-density suspension culture in vaccine production.

International Journal of Molecular Sciences doi: 10.3390/ijms27104314

Authors: Jun Nakamura Genichi Tajima Makiko Suwa Chikara Sato

How do ryanodine receptors (RyRs) open simultaneously to trigger the contraction of whole myofibrils within a large skeletal muscle cell? One possible answer is the uniformity of mechanosensitive RyRs, which is mechanically forced by the neighboring environment, including proteins. Here, we review papers addressing this proposed “mechanical sarcoplasmic reticulum (SR) paradigm”. Crystals of the molecular complexes comprising RyR and L-type voltage-gated Ca2+ channels were observed at the T-tubule/SR junction in situ using cryo-electron tomography. Observations of the SR vesicles isolated from rabbit and scallop cross-striated muscles using negative staining and transmission electron microscope raised a hypothesis of dynamic rearrangement of the Ca2+-ATPase (ATPase) molecules in response to cytoplasmic calcium concentration, as follows: (i) At a low calcium concentration where the ratio of operating ATPase molecules to the total molecules is at a submaximal level, the ATPase molecules form, at least in part, their cylindrical crystals in the SR membrane with the help of ATP; this results in the elongation of the SR vesicles. (ii) High concentrations of calcium, at which the ratio of operating ATPase molecules is maximal, reversibly collapse the ATPase crystals to transform the elongated vesicles into round forms comprising tightly attached crystal patches. These data further lead to the idea that the reversible growth of cylindrical ATPase crystals provides a dynamic crystalline network, which acts as an “SR membrane-endoskeletal motor” to manipulate the SR movement. The possibility of interactions between ATPase crystals and neighboring RyR crystals is also discussed.

International Journal of Molecular Sciences doi: 10.3390/ijms27104311

Authors: Liva Caikovska Alberts Veitners Diana Lavrinovica Juris Vanags Kristaps Klavins Guna Laganovska Arturs Zemitis

Glaucoma remains a primary cause of blindness, yet its pathogenesis often extends beyond intraocular pressure (IOP). This review integrates four converging lines of metabolic evidence—aqueous humor (AH) metabolomics, kynurenine pathway (KP) activity, tetrahydrobiopterin (H4BIP) biology, and NAD/one-carbon dysfunction—into a testable framework for retinal ganglion cell vulnerability. By utilizing a systematic AH metabolomics atlas covering glaucoma, pseudoexfoliation, and diabetes on a standardized HILIC-LC-HRMS platform, we demonstrate that, while aromatic amino acid elevations are non-specific markers, kynurenine monooxygenase (KMO) upregulation is a condition-specific glaucoma signature. These local findings are corroborated by systemic evidence: POAG patients exhibit significant folic acid deficiency (p = 0.007) and elevated alpha-1-antitrypsin (AAT). Critically, AAT correlates inversely with both serum folate (rs = −0.485, p < 0.001) and retinal nerve fiber layer thickness (rs = −0.386, p = 0.017), providing the first in-patient evidence linking systemic inflammation to structural optic nerve damage. We conclude that KMO serves as a critical enzymatic node linking tryptophan metabolism, H4BIP availability, and NAD synthesis. These results characterize glaucoma as a disease of progressive cofactor failure and define a research agenda for multimodal metabolic neuroprotection.

International Journal of Molecular Sciences doi: 10.3390/ijms27104312

Authors: Danijela Cvetković Marina Gazdić Janković Marina Miletić Kovačević Amra Ramović Hamzagić Irena Urošević Vesna Rosić Biljana Ljujić

Lipoblastomas are rare, benign tumors arising from embryonic white fatty precursor cells that continue to proliferate in the postnatal period. We present a case of a minimally differentiated lipoblastoma with myxoid features. Our patient was an 18-month-old female with a painless solid tumefaction in the middle third of the right leg. Histopathologically, the nodular tumor mass consisted of lipoblasts embedded in a myxoid stroma. Immunohistochemistry showed strong diffuse positivity for S100, CD34, CD56, NSE and rare Ki67+ cells. FOXO1 polyploidy was detected in 30% of cells by FISH. Using target RNA sequencing, we detected a CHCHD7::PLAG1 fusion gene showing that the first exons of CHCHD7 were fused to either exon 2 or exon 3 of PLAG1. Our case demonstrates that due to the histomorphologic overlaps, the molecular diagnostics can be essential for the confirmation of the diagnosis of lipoblastoma.

International Journal of Molecular Sciences doi: 10.3390/ijms27104313

Authors: Chengzhi Liu Xiaohui Wang Yu Sun

GJB2-associated hearing loss is the most common form of non-syndromic hereditary deafness worldwide. However, it exhibits significant heterogeneity in terms of both clinical presentation and biological basis. This review focuses on mechanism-oriented therapeutic strategies for GJB2-associated hearing loss, investigating how different types of GJB2 variants correspond to distinct clinical phenotypes and underlying pathogenic mechanisms, and aims to determine appropriate treatments. Current evidence suggests that GJB2-associated hearing loss is not solely caused by channel dysfunction resulting from gap junction defects, but rather the result of multiple pathological processes, including impaired GJB2 transcriptional regulation, cochlear developmental abnormalities, sensory epithelial degeneration and secondary damage pathways such as inflammation. Consequently, emerging therapeutic approaches can be viewed as interventions targeting specific mechanisms, including gene therapy, restoration of protein transport and pharmacological modulation of damage to the cochlear microenvironment. Overall, this review highlights the importance of aligning therapeutic strategies with specific GJB2 variants, underlying pathogenic mechanisms, and the developmental window during which cochlear injury remains biologically reversible.

International Journal of Molecular Sciences doi: 10.3390/ijms27104309

Authors: Krishani Dinali Perera Elisa Oltra Garcia Simon R. Carding

Human endogenous retroviruses (HERVs) are potential driving forces of the pathophysiology of Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), linking post-infectious immune dysfunction to chronic inflammation and immune and neurocognitive dysfunction that are hallmark features of ME/CFS. Accumulating evidence from related autoimmune diseases and cancers has shown that reactivated HERVs can contribute to disease pathogenesis by amplifying immune activation through viral protein-mediated innate sensing, long terminal repeat (LTR)-driven transcription, and disrupting epigenetic silencing. HERV signatures are therefore promising biomarkers for diagnosis, patient stratification for drug-repurposing trials, and therapy monitoring. Accumulating evidence suggests a possible correlation between HERV expression and ME/CFS symptom severity, alterations in immune phenotypes, function and inflammatory gene networks. Importantly, locus-specific HERV profiling is a promising approach for distinguishing ME/CFS from overlapping or co-morbid conditions and healthy controls. Furthermore, HERV-targeted antibodies, immune modulators, epigenetic and antiviral interventions offer promise as concomitant therapeutic strategies for ME/CFS. Additional research incorporating viromics and other-omics validation, functional assays, and HERV-stratified clinical trials is now needed to realise this potential and to transform ME/CFS from a symptom-based syndrome into a mechanism-driven, treatable condition.

International Journal of Molecular Sciences doi: 10.3390/ijms27104308

Authors: Hazal Sezginer Guler Hakan Gurkan Sinem Yalcintepe Yavuz Atakan Sezer Sernaz Topaloglu Ebru Tastekin Selcuk Korkmaz Daghan Dagdelen Engin Atli Selma Demir Nermin Tuncbilek

Triple-negative breast cancer (TNBC/18–21%) lacks targeted treatment options due to the lack of ER/PR and HER2 expression. The transport of lncRNAs via exosomes plays a role in tumor progression and metastasis and reshapes tumor-associated signaling pathways. This study aimed to compare the expression of exosomal HOTAIR, NEAT1, MALAT1, AFAP1-AS1, ANRIL, and HULC lncRNAs in primary tumor tissue and blood of patients with sporadic TNBC to evaluate their potential as biomarkers. The patients diagnosed with TNBC between the years 2021 and 2025, 21 of 62 (33.87%) with sporadic breast cancer and thirty healthy controls were included in the study. Primary tumor tissue and peripheral venous blood samples were collected from 21 patients who did not receive neoadjuvant chemotherapy. Expression levels of exosomal lncRNAs (HOTAIR, NEAT1, MALAT1, AFAP1-AS1, ANRIL, and HULC) were determined in both tissues and blood samples from the patient and control groups using Real-Time PCR method. In the patient group, HOTAIR, HULC, ANRIL, and AFAP1_AS1 gene expression was lower (downregulated) in tissue and serum compared to the control group, whereas NEAT1 and MALAT1 were higher (upregulated). Tissue and serum samples taken from the patient group were found to have statistically consistent expression levels of HOTAIR, HULC, and ANRIL genes. Furthermore, HOTAIR, HULC, and ANRIL serve as biomarkers and can be studied using exosomal RNA samples obtained from patient serum without invasive procedures. Our current study, which has different lncRNA expression profiles, reflects the biological heterogeneity of TNBC and contributes to a better understanding of its subtypes at the molecular level.

International Journal of Molecular Sciences doi: 10.3390/ijms27104307

Authors: Nayan De Jhuma Bhadra Md Sorique Aziz Momin Kamala Mitra Debmalya Bhunia Achinta Sannigrahi

This review investigates biomaterial-based strategies for improved treatment of MPXV. We focus on emerging synthetic biomedical approaches to combating the virus. These include peptide nucleic acids, CRISPR-based systems, and small-molecule therapeutics. These methods work by targeting and blocking viral proteins and enzymes. Such synthetic platforms may help reduce viral transmission and minimize side effects. They also offer potential solutions to challenges such as viral resistance in humans. In addition, biomaterials contribute to the development of more stable and effective vaccines. Combining these biomaterials with mRNA technology provides a promising framework for future vaccine development. Overall, this review underscores biomaterial-driven antiviral systems as a major frontier in translational medicine with profound implications for global health and pandemic awareness.

International Journal of Molecular Sciences doi: 10.3390/ijms27104306

Authors: Tomasz Kowalczyk Maciej Kowalski Adam Majchrzak Laurent Picot Lucyna Herczyńska Wirginia Kukula-Koch Noureddine El Aouad Przemysław Sitarek

The growth of pistachio (Pistacia spp.) production, particularly in America, Iran, and Turkey, has resulted in the production of substantial quantities of by-products, including shells, fruit husks, leaves, resins, and tree pruning waste. Although these fractions contain a range of beneficial secondary compounds, they are rarely used. Recent advances in nanotechnology and materials engineering suggest that they can be used as inexpensive, renewable raw materials in the fields of agriculture, the food industry, cosmetics, pharmaceuticals, and environmental engineering. Pistachio by-products have been shown to exhibit antioxidant, antibacterial, antifungal, and anticorrosive properties, making them good candidates for use in active packaging systems and nanoencapsulation. They may also be valuable as fertilisers, animal feed, and composite materials. They have been found to have potential roles in industrial pollutant removal and energy storage, and as ‘green’ precursors for nanomaterials. This review summarises the current knowledge on the multifunctional applications of Pistacia spp. by-products, emphasising their importance in implementing circular economic strategies and sustainable industrial development. This study also addresses the practical application of pistachio by-products, as well as the widely appreciated nuts, within the domain of patents, thereby illustrating the prospective pathway of currently emerging solutions in the context of sustainable development.

International Journal of Molecular Sciences doi: 10.3390/ijms27104304

Authors: Jenjira Wongdee Teerana Greetatorn Pongdet Piromyou Pongpan Songwattana Natcha Pruksametanan Neung Teaumroong Nantakorn Boonkerd Pakpoom Boonchuen Eric Giraud Panlada Tittabutr

In this study, we investigate two RpoN homologs in Bradyrhizobium sp. DOA9—chromosomal RpoNc and megaplasmid-borne RpoNp—and their roles in free-living conditions and nitrogen fixation. Phylogenetic analysis showed that RpoNc clusters with RpoN proteins from symbiotic nitrogen-fixing strains, whereas RpoNp forms a distinct clade, consistent with a function in stress responses. RpoNc proved essential for free-living conditions: ΔrpoNc mutants displayed severe growth defects that RpoNp could not compensate for. Transcriptomic comparisons between wild type and mutant RpoN identified 541 differentially expressed genes (DEGs) grouped into three clusters: 100 downregulated, 175 upregulated, and 254 moderately downregulated (with a fold change > 2, and a q-value (FDR, padj) < 0.05). Affected pathways involved nitrogen metabolism, motility, and environmental adaptation. RpoNc controlled major nitrogen fixation genes (nif and fix) along with core growth and stress response functions, while RpoNp mainly influenced stress-adaptation pathways. Genome-wide promoter motif analysis predicted 68 putative RpoNc targets, mainly associated with nitrogen fixation and metabolism, compared with only 22 predicted RpoNp targets, indicating a more restricted regulon. Electrophoretic mobility shift assays (EMSAs) further confirmed that both RpoN proteins directly bind σ54-dependent promoters identified from transcriptomic data, supporting their regulatory roles under free-living conditions. Two mutants (ΔrpoNc and ΔrpoNp::ΩrpoNc) showed broad transcriptional disruption across nitrogen fixation, metabolism, and stress responses, underscoring complementary regulation. Overall, RpoNc is the dominant regulator of nitrogen fixation and core metabolism during free-living conditions, whereas RpoNp fine-tunes stress responses, revealing new regulatory insights for DOA9 adaptation. These results clarify how RpoN systems optimize survival across fluctuating conditions.

International Journal of Molecular Sciences doi: 10.3390/ijms27104305

Authors: Chintan Chawda Giorgia Zambito Natasa Gaspar Christopher Schliehe Pieter J. M. Leenen Clemens Löwik Laura Mezzanotte

Macrophages play a crucial role in health and disease. Currently, reporter mice for tracking alternatively activated macrophages in vivo are lacking. We designed a transgenic mouse model in which luminescence and fluorescence proteins, click beetle red luciferase (CBRED2) and mKate2, report on the expression of the Mrc1/Cd206 promoter, active in the monocyte/macrophage population. The mouse line was named B6Mrc1-mKate2-CBRED2. Using this novel mouse model, we were able to develop in vitro assays to validate transgenic macrophage polarization and test them with compounds of repolarization potency. Furthermore, in the in vivo assays, we exploited the migratory and infiltrative potency of macrophages for detecting tumor locations via optical imaging. In fact, macrophages can act as universal cancer markers, as they infiltrate primary and secondary tumors, stimulating or suppressing tumor growth. We first characterized transgenic mice for reporter expression ex vivo, followed by the generation of luminescence-based assays to reflect the polarity of differentiated macrophages, and lastly, we visualized reporter macrophages accumulating and infiltrating the tumor microenvironment (TME) of murine pancreatic ductal adenocarcinoma (PDAC) at multiple time points. We found that the extent of macrophage recruitment and retention was dependent on the infiltrative T-cell and dendritic cell populations present in the TME, reflecting the immunologically hot or cold nature of the PDAC clones, respectively. In conclusion, the ability to optically detect light-emitting macrophages can be applied not only for cancer studies but also in the context of inflammatory diseases.

International Journal of Molecular Sciences doi: 10.3390/ijms27104300

Authors: Xiaolong Wu Dong Liu Haoming Geng Binghan Zhang Huantong Diao Yiqiang Zhou Gang Song Ye Cheng Jiantao Liang

Synaptogenesis-related neuron–glioma interactions are increasingly recognized in glioma, yet it remains unclear whether routine H&E morphology can capture these programs and improve prognostic stratification. We integrated H&E whole-slide images, transcriptomes, and clinical data from 434 TCGA gliomas. Deep learning and quantitative pathology yielded an integrated histomorphologic feature set of 2678 features. Synaptogenesis-related activity was quantified using ssGSEA for ninety-eight synaptogenesis-related factor genes. In the training cohort, Spearman analysis identified 149 correlated histomorphologic features, which were refined to thirty-five by elastic net regularization. Seventeen prognostic candidates were entered into the MIME1 framework, and the most parsimonious model, Enet[0.1], retained fourteen non-zero-coefficient features to define the synaptogenesis-associated histomorphologic signature and construct the pathology-derived risk score (PRS). Multi-omic analyses, Human Protein Atlas validation, and single-nucleus RNA-seq were used to investigate the hub gene and its cellular context. PRS robustly stratified survival in both training and validation cohorts and remained an independent prognostic factor after adjustment for age and 2021 WHO CNS grade. High-risk tumors showed increased stromal and immune scores and enrichment of immune, adhesion, and phagosome-related pathways. EFNB2 emerged as the hub gene and was enriched in glioblastoma, and EFNB2-positive malignant cells displayed prominent communication with neurons, including EFNB2-EPHB1 signaling. Exploratory re-analysis of the myeloid compartment further showed that glioblastoma was enriched for suppressive TAM-like states relative to astrocytoma grade 2, supporting a shift toward a more tumor-associated and potentially immunosuppressive microenvironment. Routine H&E histomorphology can capture synaptogenesis-related molecular programs in glioma. The resulting PRS provides clinically relevant prognostic stratification, while EFNB2-positive malignant cells may represent a candidate hub for neuron–tumor communication within a remodeled tumor ecosystem.

International Journal of Molecular Sciences doi: 10.3390/ijms27104303

Authors: Takashi Oda Iroha Okano Hiyori Takahashi Azumi Nara Sachiko Iwama Takahiro Uchida Muneharu Yamada Kazuo Yamakami Tadasu Kojima

Circulating immune complexes (CICs) are frequently detected in the sera of patients with myeloperoxidase (MPO)–antineutrophil cytoplasmic antibody (ANCA)-associated glomerulonephritis (MPO-AAGN) and their role in activating the classical complement pathway has been suggested. However, the precise composition and functional characteristics of CICs in AAGN remain poorly understood. We analyzed serum samples from four patients with MPO-AAGN and confirmed CICs. An immunoadsorbent column was prepared using a monoclonal rheumatoid factor antibody that binds to CICs, enabling extraction via immunoprecipitation. CICs were analyzed by Western blotting to detect MPO and IgG. Their capacity to activate complement was assessed in vitro by measuring complement activation products using the enzyme-linked immunosorbent assay following incubation with normal human serum. Western blotting revealed distinct bands for both MPO and IgG in all samples. Incubation of extracted CICs with normal human serum resulted in elevated levels of complement activation products, including C5a and C5b-9. This increase was completely inhibited by the addition of EDTA or EGTA. In conclusion, CICs in the serum of patients with MPO-AAGN contain MPO and IgG (presumably MPO-ANCA). These CICs can activate the complement system, likely through the classical pathway. Our findings support the hypothesis that CICs composed of MPO and MPO-ANCA contribute to complement activation via the classical pathway and play a significant role in AAGN pathogenesis.

International Journal of Molecular Sciences doi: 10.3390/ijms27104302

Authors: Piotr Pawlik Grażyna Kurzawińska Marcin Ożarowski Tomasz M. Karpiński Anna Bogacz Piotr J. Olbromski Aleksandra E. Mrozikiewicz Maciej Brązert Wiesław Markwitz Agnieszka Seremak-Mrozikiewicz

We investigated five single-nucleotide variants (SNVs) of the FN1 gene in female reproductive organ cancers. The proteins expressed by this gene are essential components of the extracellular matrix (ECM) that constitutes the tumor microenvironment (TME). The study group included 208 women diagnosed with cervical, uterine, and ovarian cancers and 208 age-matched cancer-free controls. Genomic DNA from whole blood was used to analyze five intronic SNVs of the FN1 gene using PCR/RFLP. The results indicate that two of the studied FN1 gene variants may increase the risk of gynecological cancers in dominant and log-additive models (p = 0.048 and p = 0.040 for rs6725958, p = 0.033 and p = 0.038 for rs1968510, respectively). Comparing individual cancer groups with the controls, differences were observed for the ovarian cancer group (rs1968510 p = 0.015 and p = 0.016, rs6725958 p = 0.070 and p = 0.037 in dominant and log-additive models, respectively). None of these associations remained statistically significant after Bonferroni correction for multiple testing. Haplotype analyses revealed that the AGATC haplotype, containing minor alleles for rs35343655 and rs6725958, was more frequent in the entire gynecological cancer group (p = 0.0036). For individual cancer types, values of p = 0.0071 for ovarian, p = 0.0028 for endometrial, and p = 0.0269 for cervical cancers were obtained; Our preliminary study suggests that the rs6725958 and rs1968510 FN1 variants may slightly increase the risk of female reproductive system cancers, particularly ovarian cancer. These findings require further validation in larger, independent cohorts and functional studies.

International Journal of Molecular Sciences doi: 10.3390/ijms27104299

Authors: Barbara Seliger Rene Mantke Norbert Naß Werner Dammermann Soeren Ocvirk Janine Kah Thomas Kalinski Chiara Massa

Colorectal cancer (CRC) is a significant global health concern, ranking as the third most frequently diagnosed cancer and the second leading cause of cancer-related deaths. Advances in screening, such as the implementation of liquid biopsies (LB), have improved early detection, thus enhancing survival rates. This review summarizes the multifaceted nature of CRC, focusing on its genetic background, the complex tumor microenvironment, and the influence of gut microbiota, nutrition, and metabolic alterations. The development of CRC is influenced by various risk factors, including age, genetics, chronic diseases, and lifestyle choices. The genetic heterogeneity of CRC defines distinct molecular subtypes, characterized by different treatment responses and patient prognoses. Chronic inflammation and dysbiosis in the gut microbiota further contribute to CRC pathogenesis. In addition, nutritional factors play a crucial role in CRC, affecting carcinogenesis and treatment efficacy through direct interaction with the immune system and microbiome. Current therapeutic strategies include surgical interventions, chemo- and radiotherapy, targeted therapies, immunotherapy as well as dietary interventions, and microbiome modulation, highlighting the challenges posed by tumor heterogeneity and treatment resistance. In sum, a comprehensive understanding of CRC’s intrinsic and extrinsic drivers, including genetic, metabolic, and dietary influences, is essential for developing personalized treatment strategies and improving patient outcomes.

International Journal of Molecular Sciences doi: 10.3390/ijms27104301

Authors: Kristina Mikhalchuk Svetlana Artemieva Viktoria Zabnenkova Maria Akhkiamova Elena Dadali Galina Rudenskaya Peter Sparber Olga Rybakova Yulia Papina Anastasiya Monakhova Irina Shulyakova Dmitriy Saiko Svetlana Zhiteneva Alexander Polyakov Olga Shchagina

Spinal muscular atrophy 5q (5q SMA) is one of the most prevalent autosomal recessive disorders globally. The underlying cause of 5q SMA is attributed to variants in SMN1. To date, there are no reported cases of gene-based therapy in rare patients with 5q SMA caused by subtle SMN1 variants of unknown clinical significance. We included 10 patients with the clinical manifestations of 5q SMA associated with intragenic variants in combination with a heterozygous SMN1 deletion in this retrospective study. Previously reported pathogenic or likely pathogenic variants were identified (e.g., c.*3+1del, c.815A>G (p.Tyr272Cys), and c.821C>T (p.Thr274Ile)). Variants of unknown clinical significance were also found, including a recurrent, previously unreported variant c.80A>C (p.Gln27Pro). We also report detailed molecular genetic and clinical data on 9 patients with 5q SMA. In addition, we provide results from the cohort of patients with gene-based therapy, consistent with data from patients with a homozygous SMN1 deletion.

International Journal of Molecular Sciences doi: 10.3390/ijms27104298

Authors: Muhammad Umair Khan Ľuboš Danišovič Jaroslav Katrlík

Glycosylation is a critical determinant of extracellular vesicle (EV) biology, shaping vesicle biogenesis, stability, biodistribution, cellular recognition, and uptake. Because EV glycans mirror disease-associated remodeling of parental cells, EV glycosylation is emerging as both a rich source of biomarkers and a functional regulator of regenerative signaling. This review highlights how altered EV glycosylation generates disease-specific signatures across major cancers, including lung, hepatocellular, colorectal, bladder, ovarian, pancreatic, and prostate cancer, and also discusses evidence in neurological, neuropsychiatric, metabolic, autoimmune, urinary, and musculoskeletal disorders. Beyond diagnostics, we examine the growing role of EV glycosylation in regenerative medicine, where glycan-dependent targeting and tissue interactions contribute to neural, cardiac, renal, skeletal, joint, and skin repair. We further provide an integrated overview of analytical strategies for EV glycosylation research, spanning mass spectrometry-based glycomics and glycoproteomics, affinity-based profiling, lectin microarrays, imaging, spectroscopic methods, advanced biosensing and nanotechnology-based approaches, and emerging artificial intelligence and bioinformatics tools. Current methodological challenges, biosafety issues, translational barriers, and future technologies are also critically discussed. Altogether, this review positions EV glycosylation as a promising interface between EV biology, precision diagnostics, and next-generation regenerative therapeutics.

International Journal of Molecular Sciences doi: 10.3390/ijms27104297

Authors: Jie Wang Sijia Yang Xiaoheng Wang Yi Chang Fan Yang Panpan Qiang Xiangting Wang Tatsuo Shimosawa Qingyou Xu Yunzhao Xiong

Fibroblasts and lymphangiogenesis promote renal fibrosis. However, whether fibroblasts promote renal fibrosis via lymphangiogenesis has not yet been fully elucidated. This study set out to clarify whether aldosterone induces fibroblast transdifferentiation into lymphatic endothelial-like cells, thus promoting lymphangiogenesis and renal fibrosis. In vivo, twenty-four male Wistar rats were randomized into Sham, ALD (6-week aldosterone infusion), and ALD + ESA (aldosterone infusion with esaxerenone co-treatment) groups. In vitro, primary rat renal interstitial fibroblasts (RKFs) were used. Immunohistochemistry and Western blot were used to detect lymphatic endothelial and fibroblast marker expression in kidneys from aldosterone-infused rats and RKFs. Their co-expression was determined by flow cytometry and immunofluorescence co-staining. Mineralocorticoid receptor (MR) activation and related signaling pathways were also analyzed by Western blot, immunohistochemistry, and flow cytometry. Additionally, RKF migration and tube formation were examined to investigate the role of aldosterone-induced fibroblast-to-lymphatic endothelial-like transdifferentiation in renal fibrosis. Our data suggest that aldosterone activates the MR and induces the transdifferentiation of fibroblasts into lymphatic endothelial-like cells via the MR/VEGFC/VEGFR-3 pathway, thereby promoting lymphangiogenesis. In addition, the administration of esaxerenone (a mineralocorticoid receptor blocker, MRB) to rats significantly suppresses this transdifferentiation and alleviates fibrosis.

International Journal of Molecular Sciences doi: 10.3390/ijms27104293

Authors: Stefania Elena Navone Laura Guarnaccia Massimiliano D. Rizzaro Laura Begani Emanuela Barilla Giovanni Alotta Emanuele Garzia Manuela Caroli Antonella Ampollini Aniello Violetti Noreen Gervasi Rolando Campanella Laura Riboni Marco Locatelli Giovanni Marfia

In the original publication [...]

International Journal of Molecular Sciences doi: 10.3390/ijms27104295

Authors: Simona Mrakic-Sposta Maristella Gussoni Federica Mrakic-Sposta Guido Giardini Lorenza Pratali Michela Montorsi Alessandro Tonacci Cinzia Dellanoce Massimo Martinelli Alessandra Vezzoli

This study investigates the bio-physiological responses occurring under extreme stress conditions and the characterization of the oxy-inflammatory profile of Finishers (FRs) and NoFinishers (NFRs) athletes during the time course and following the Transpyrénéa, an 866 km extreme ultra-race across the French Pyrenees with an altitude difference of 52,900+ m ascent. Thirty-nine experienced ultra-marathon runners (age 43.5 ± 9.1 years; weight 72.1 ± 11.1 kg; BMI 23.3 ± 2.6 kg/m2) were studied using minimally invasive methods on capillary blood and urine samples obtained at baseline (T0), during (T1, 2, 3) and at the end (T4) of the race. Reactive Oxygen Species (ROS) production, total antioxidant capacity (TAC), oxidative damage (8-hydroxy-2-deoxy Guanosine: 8-OH-dG and 8-isoprostane: 8-isoPGF2α), inflammatory (IL-6), nitric oxide pathway (NOx and 3-NT), neopterin, and hematologic (lactate, and hematocrit) biomarkers were assessed. In both FR and NFR athletes a marked systemic increase in ROS, oxidative and nitrosative damage, inflammation, transient immune-renal dysfunction and lactate release were detected throughout the race. Compared to FRs, NFRs displayed significant differences concerning ROS production at T0, 8-isoPGF2-α at T0, T1 and T2, and perceived exertion (RPE score) at T2. These data potentially reflect enhanced adaptative responses to training and metabolic efficacy in FRs, allowing them to better tolerate extreme physiological stress.

International Journal of Molecular Sciences doi: 10.3390/ijms27104296

Authors: Alexis Cho Chunjing Wu George Theodoropoulos Manojavan Nagarajan Adeline M. Murphy Karli F. Heller Niramol Savaraj Theodore J. Lampidis Medhi Wangpaichitr

Tryptophan (Trp) metabolism sits at the intersection of nutrition, the microbiome, mucosal immunity, and tumor adaptation. The broad observation that microbial indoles can support barrier function, whereas tumors exploit kynurenine-pathway metabolism to suppress immunity, is already established in publications. The specific contribution of this review is to organize that literature into a context- and network-based translational framework. Rather than treating indoleamine 2,3-dioxygenase 1 (IDO1) as a single bottleneck, we frame tumor Trp metabolism as a compensatory system linking IDO1, tryptophan 2,3-dioxygenase (TDO2), interleukin-4-induced gene 1 (IL4I1), amino-acid transport, amino-acid stress sensing, and downstream aryl hydrocarbon receptor (AHR) signaling. In healthy tissue, especially the gut, dietary Trp and microbiota-derived indoles can promote epithelial integrity, interleukin-22 (IL-22)-associated programs, and mucosal restraint. In tumors, the same substrate pool is redirected toward Kynurenine, kynurenic acid, indole-3-pyruvate, and related catabolites that impair cytotoxic lymphocytes, expand regulatory T-cell (Treg) and suppressive myeloid compartments, and reinforce invasion and treatment resistance. We also argue that the potential metabolite biomarker interpretation should be context-dependent. Finally, we propose a clinical-context–specific framework for intervention. Dietary and microbiome-based strategies may be most effective in prevention, premalignant states, or supportive care, whereas established cancers are more likely to require biomarker-guided targeting of tumor-associated catabolic pathways and convergent signaling mechanisms. The “paradox” is therefore not that Trp changes chemistry across settings, but that the same nutrient is routed through different cellular contexts, enzymes, ligands, and cell states.

International Journal of Molecular Sciences doi: 10.3390/ijms27104294

Authors: Samuele Roncareggi Francesca Fioredda Katia Girardi Simone Serrao Giulia Capitoli Rebecca Fumagalli Marta Nobile Grazia Fazio Fabiola Guerra Maria Grazia Valsecchi Stefano Rebellato Marika Casillo Maria Rosaria Fantuz Giovanni Savarese Giuseppe Paglia Eleonora Gambineri Adriana Cristina Balduzzi Andrea Biondi Francesco Saettini

GATA2 deficiency predisposes patients to recurrent infections, myelodysplastic neoplasms (MDSs), and malignancies through disrupted hematopoiesis and immune dysfunction. The role of the gut microbiome (GM) in this condition remains poorly defined. In this multicenter study, we analyzed GM composition, metabolomic, and lipidomic profiles in 12 Italian GATA2-deficient patients, comparing non-HSCT and post-HSCT GATA2-deficient individuals with healthy controls. Non-HSCT patients showed a relative enrichment of Proteobacteria-associated Gram-negative taxa, accompanied by increased levels of metabolites and lipids previously associated with inflammatory processes. Post-HSCT patients displayed profiles with a trend toward partial normalization of GM composition and metabolic features. Overall, our findings suggest the presence of microbiome and metabolic patterns in GATA2-deficient patients, which may reflect underlying immune and hematopoietic alterations, although these observations should be interpreted as descriptive and require validation in larger cohorts.

International Journal of Molecular Sciences doi: 10.3390/ijms27104289

Authors: Francisca Villarroel Eder Ramírez Nikol Ponce Francisco Nualart Felipe Ramírez-Cepeda Luis Mercado Maria Angélica Miglino Paulo Salinas

Chronic exposure to fine particulate matter (PM2.5) derived from residential wood combustion is a major environmental health concern in southern Chile and other cold-climate regions. Although PM2.5 has been linked to adverse reproductive outcomes, it remains unclear whether sustained exposure induces pregestational uterine alterations that compromise reproductive competence before the first pregnancy. This study evaluated the effects of chronic wood smoke-derived PM2.5 exposure on uterine morphology and molecular markers in nulliparous rats. A two-generation exposure model was used to assess cumulative effects. Second-generation (G2) female Sprague Dawley rats continuously exposed from conception were housed in filtered air (FA, control; n=12) or PM2.5-containing ambient air (NFA; n=12) until reproductive maturity (82 days). Uterine horns were analyzed by histology, planimetry, immunohistochemistry, immunofluorescence, and second harmonic generation microscopy. Markers of hypoxia, inflammation, extracellular matrix remodeling, angiogenesis, proliferation, apoptosis, and DNA repair were quantified. Chronic PM2.5 exposure increased hypoxia-inducible factor 1α, tumor necrosis factor-α, vascular endothelial growth factor A, and collagen types I, III, and IV, while transforming growth factor-β expression and Ki-67-positive proliferating cells were reduced. Exposed rats showed increased apoptosis and decreased nuclear expression of O6-methylguanine-DNA methyltransferase, indicating impaired DNA repair capacity. Second harmonic generation imaging demonstrated increased collagen deposition with marked fibrillar disorganization. These findings indicate that chronic wood smoke-derived PM2.5 exposure induces hypoxia-driven structural and molecular alterations in the uterus of nulliparous rats before first pregnancy, including extracellular matrix remodeling, inflammatory imbalance, angiogenic dysregulation, reduced proliferation, and compromised DNA repair, suggesting early disruption of uterine homeostasis and increased susceptibility to adverse reproductive outcomes.

International Journal of Molecular Sciences doi: 10.3390/ijms27104292

Authors: Daniil Shepilov Dana Askarova Anar Seisembekova Seitzhan Turganbay Ardak Jumagaziyeva Tamara Bukeyeva Gulnara Yuldasheva Nurdaulet Temir Lyudmila N. Ivanova Natalya Zubenko Sabina Kenesheva

Due to the increasing threat of antibiotic resistance and the emergence of new pathogenic strains, the development of effective combined therapeutic agents represents a crucial direction in the fight against infections. Within this study, several compounds were synthesized in which iodine is present in a coordination complex with antibiotics—sodium sulfadimidine and gentamicin sulfate. The physicochemical parameters of these compounds were investigated using capillary electrophoresis and UV spectroscopy, along with their cytotoxicity, antimicrobial, and antiviral activities. As a result of this work, two stable compounds, KC-246 and KC-248, were synthesized, demonstrating virus-inhibitory activity against herpes simplex virus and influenza A under extremely low cytotoxicity levels of 0.018–0.106 mg/mL. Additionally, they exhibited antimicrobial activity against representatives of the families Staphylococcaceae, Pseudomonadaceae, Enterobacteriaceae, Enterococcaceae, and yeast-like fungi. The minimum bactericidal concentrations (MBCs) ranged from 0.794 µg/mL to 0.198 µg/mL (KC-246) and from 2.093 µg/mL to 0.523 µg/mL (KC-248).

International Journal of Molecular Sciences doi: 10.3390/ijms27104291

Authors: Yong-Xiao Wang Ed Wilson Santos Sarahann Mistretta Yuexing Yuan Harold A. Singer Shey-Shing Sheu Yun-Min Zheng

Type-1 ryanodine receptor (RyR1) is essential for skeletal muscle contraction. This Ca2+ release channel is expressed in cardiac myocytes; however, its function remains elusive. Cardiac-specific RyR1 overexpression (OE) mice were generated under the cardiac-specific Myh6 promoter. Cardiac hypertrophy (CH), cardiac functions, and mechanistic changes in RyR1 OE and control (wildtype, WT) mice were assessed using hematoxylin and eosin staining, echocardiography, electrocardiogram, quantitative RT-PCR, Western blotting, [3H]-ryanodine binding assay, confocal microscope, ROS dye Amplex Red and 2′,7′-dichlorofluorescein diacetate. RyR1 OE mice had increased whole heart, left ventricular weight, and left ventricular wall thickness, but decreased cardiac output and stroke volume, thereby presenting CH and heart failure (HF). CH markers like ANF, BNF, and aSKA mRNAs were increased in RyR1 OE heart. RyR1, but not RyR2 or RyR3, expression was increased in the RyR1 OE mouse heart. Similar results were found in mice with TAC-induced CH. RyR1, but not RyR2 mRNA, was increased in cardiac muscle from dogs and humans with CH and/or HF. Maximum [3H]-ryanodine binding was increased, whereas the binding dissociation constant decreased in left ventricular cardiomyocytes from RyR1 OE mice. RyR2-dependent Ca2+ sparks were increased, which was blocked by riluzole, a small molecule known to inhibit RyR2. Consistently, ROS was remarkably increased in RyR1 OE cardiac cells. We first generated cardiac-specific RyR1 OE mice; these mice had CH, HF, and increased RyR1 expression with no RyR2 or RyR3 alteration. Similar changes were observed in mice, dogs, and humans with CH and HF. Increased mitochondrial ROS-dependent RyR2 Ca2+ release was essential for RyR1-induced CH and HF.

International Journal of Molecular Sciences doi: 10.3390/ijms27104290

Authors: Yuko Yokohama Yugo Watanabe Ke-ichi Nakajima Akihiro Umezawa Satoru Takahashi Yasuhiro Mori Yasuhito Kato Jun-ichi Kawabe Takashi Yazawa

The placenta produces a variety of steroid hormones through the catalytic activity of steroidogenic enzymes, including cytochrome P450 (CYP) hydroxylases and hydroxysteroid dehydrogenases (HSD). Large amounts of progesterone produced by the placenta are essential for the maintenance of pregnancy. Although androgens and estrogens are also elevated in maternal circulation during gestation, there are conflicting reports on whether de novo synthesis of these steroids occurs in the human placenta. To address this issue, we performed a comprehensive analysis of steroidogenic gene expression in early and term placenta. While none of the genes examined showed binary expression changes, 17β-HSDs, including HSD17B1 and AKR1C3, were markedly upregulated in the term placenta. CYP19A1 and HSD11B2 genes were also markedly upregulated. In contrast, CYP17A1, CYP21A2, CYP11B1, CYP11B2, and HSD17B3 were almost undetectable. Consistent with these findings, the plasma ratios of active to precursor sex steroids (estradiol/estrone and testosterone/androstenedione) were higher in pregnant than in non-pregnant women, although concentrations of all steroids increased. In contrast, plasma levels and profiles of 11-oxygenated androgens were unchanged. These results indicate that the human placenta does not significantly contribute to circulating levels of either classical or novel classes of androgens. Therefore, this study provides new insights into the tissue of origin and the physiological significance of sex steroids during gestation.

International Journal of Molecular Sciences doi: 10.3390/ijms27104288

Authors: Liberty T. Navhaya Mokgerwa Z. Monama Thabe M. Matsebatlela Xolani H. Makhoba

Coronavirus disease 2019 continues to pose global health challenges, with the pandemic significantly burdening several economies, healthcare systems, and the social lives of individuals. Furthermore, new cases continue to be reported, underscoring the need for therapeutic strategies targeting conserved regions and host–virus interactions. Building on earlier virtual screening for small molecules, all-atom molecular dynamics simulations and binding-free-energy calculations were performed to elucidate how the two previously identified small molecules (NSC36398 and NSC281245) may affect the dynamic behaviour of the interaction between heat shock 70 kDa protein 8 (HSPA8) and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein. Post-MD analyses refined prior docking predictions, where NSC281245 was found to bind tightly to the complex with limited perturbations at the HSPA8-spike protein interaction surface, whereas NSC36398 appeared to induce allosteric-like domain-level destabilisation effects while maintaining stable polar contacts with the protein. Our findings demonstrate the potential of NSC36398 as a promising modulator for disrupting the HSPA8-spike protein complex, which may serve as a structural lead for designing next-generation inhibitors of host–virus interactions.

International Journal of Molecular Sciences doi: 10.3390/ijms27104287

Authors: Tong Pei Guanyue Su Jie Yang Wenbo Gao Xinrui Yang Yaojia Zhang Jie Ren Yang Shen Xiaoheng Liu

In the original publication [...]

International Journal of Molecular Sciences doi: 10.3390/ijms27104286

Authors: Linaloe Manzano-Pech María Elena Soto Vicente Castrejón-Tellez Elizabeth Soria-Castro Verónica Guarner-Lans Sara Caballero-Chacón Raúl Martínez-Memije Juan Carlos Torres-Narváez Mohammed El-Hafidi Israel Pérez-Torres

The response to the comment regarding our article is accurate: chronic consumption of a 6% Hibiscus sabdariffa Linnaeus (HSL) infusion for one month in healthy rats reduces reactive oxygen species (ROS) [...]

International Journal of Molecular Sciences doi: 10.3390/ijms27104285

Authors: Johnny Thai Nguyen Phuong Phoebe Pham Liang-Jun Yan

Reductive stress is the opposite of oxidative stress but can transition to oxidative stress [...]

International Journal of Molecular Sciences doi: 10.3390/ijms27104284

Authors: Sarah Almofty Vijaya Ravinayagam Hatim Dafalla B. Rabindran Jermy

Halloysite nanotubes (HNTs), composed of an aluminosilicate framework, are naturally abundant, biocompatible, and sustainable clay minerals with a tubular morphology and tunable surface chemistry, making them attractive platforms for targeted, multifunctional drug delivery systems. In this study, a zinc ferrite integrated halloysite nanocomposite (ZnFe2O4/HNT) was developed via a one-pot synthesis approach for sustained release of cisplatin (Cp), aiming to reduce systemic toxicity and enhance cell-specific activity. The nanocomposites were further functionalized by integrating Cp (Cp: ZnFe2O4/HNT ratio 0.05) and folic acid (ZnFe2O4/HNT/Cp: FA ratio 0.05), followed by PEGylation (0.17 µL/mg of ZnFe2O4/HNT/Cp/FA/PEG). The structural and surface characteristics, phase, interfacial interactions (FA and Cp), and colloidal stability of nanoformulations were systematically investigated using powder X-ray diffraction analysis (XRD), Fourier transformed infrared (FT-IR) spectroscopy, zeta potential analysis, scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS), high-resolution transmission electron microscopy (HRTEM), and diffuse reflectance UV–visible (DRS-UV-Vis) spectroscopy. The results confirmed that ZnFe2O4 integration preserved the clay’s tubular framework while inducing nanocrystallization of both ferrite and cisplatin, indicating molecular dispersion within the clay matrix. Functionalization with FA (ZnFe2O4/HNT/Cp/FA) promoted amide bond linkage, modulated Cp-FA interactions, and significantly enhanced cumulative Cp release compared to the non-functionalized system ZnFe2O4/HNT/Cp (10.3% at 72 h vs. 34.4% at 72 h) under tumor acidic conditions (pH 6.6). PEGylation maintained the controlled release profile while improving dispersion stability. In vitro cytotoxicity studies revealed that FA-conjugated nanocomposites exhibited enhanced, time-dependent anticancer activity against HeLa cervical cancer cells, with reduced toxicity toward normal fibroblasts, indicating preferential cellular uptake via folate receptor-mediated mechanism. Overall, this work demonstrates that FA-functionalized ZnFe2O4/HNT nanocomposite provides an effective clay-based platform for modulating Cp release and enhancing folate receptor protein-mediated targeted therapy for cervical cancer.

International Journal of Molecular Sciences doi: 10.3390/ijms27104282

Authors: Zorka Szollár Fanni Dzsubák Ádám Ürmös Barbara N. Borsos Balázs Bende Zoltán G. Páhi Tibor Pankotai

Tumor progression is primarily driven by DNA mutations; however, this mechanism alone does not fully account for all aspects of tumor development. Beyond genetic alterations, epigenetic changes also significantly influence the mutational landscape and affect gene expression without altering the DNA sequence. To gain a more comprehensive understanding of these regulatory mechanisms, it is essential to analyze gene expression at the transcriptional level. In this study, we examined non-small cell lung cancer (NSCLC) samples to identify specific gene expression changes, particularly in early-stage tumors. We conducted a bioinformatic analysis of RNA-sequencing data, followed by validation using an independent dataset from The Cancer Genome Atlas. Our analysis revealed a set of differentially expressed genes, seven of which were validated in patient-derived samples. Among these genes, EFNA4 and TEDC2 were significantly upregulated, whereas CDC42EP2, STX11, THBD, TMEM88, and GPM6A were notably downregulated in tumor tissues compared with adjacent normal tissues. Our findings highlight a distinct gene expression signature that differentiates NSCLC samples from normal lung tissues at the transcriptional level. These results underscore the potential of transcriptomic profiling as a promising tool for early-stage cancer detection and biomarker discovery.

International Journal of Molecular Sciences doi: 10.3390/ijms27104283

Authors: Tery Yun Junhee Park Myungin Baek

A myelination is essential for neural function in the vertebrate central nervous system, yet the molecular details of how the oligodendrocyte differentiation program has evolved remain poorly understood. Here, we performed a cross-species single-cell transcriptomic analysis of oligodendrocyte lineage cells in the spinal cord of five vertebrate species: fugu, mudskipper, chicken, mouse, and human. Pseudotime trajectory analysis revealed a shared oligodendrocyte progenitor cell (OPC) to committed oligodendrocyte precursor (COP) to myelin-forming oligodendrocyte (MOL) differentiation trajectory across all species, and CAME-based cross-species mapping confirmed the homology of OPC and MOL identities, while COP showed reduced mapping in teleosts compared with amniotes. Among stage-specific DEGs, highly shared genes (≥4 species) were organized into four co-expression modules encompassing cell projection organization, myelination, synapse assembly, and ribonucleoprotein biogenesis, with evolutionary core genes (all 5 species) enriched for oligodendrocyte differentiation and Wnt signaling. Strikingly, amniote-exclusive genes were enriched for synaptic vesicle transport, cell projection organization, predominantly at the OPC stage. This asymmetry indicates that amniotes have expanded the oligodendrocyte differentiation program at the progenitor stage, potentially linked to the myelination demands of terrestrial locomotor circuits. Our findings provide insights into how the oligodendrocyte differentiation program has been shaped by both deep evolutionary conservation and lineage-specific adaptation.

International Journal of Molecular Sciences doi: 10.3390/ijms27104281

Authors: Lucia Maria Procopciuc Gabriela Valentina Caracostea Adriana Corina Hangan Roxana Liana Lucaciu

Preeclampsia is a pregnancy-specific multisystem disorder and a major cause of maternal and perinatal morbidity and mortality worldwide. This narrative review summarizes current evidence on the principal risk factors and pathophysiological mechanisms involved in its development. The disease is best explained by the two-stage model: in stage 1, inadequate trophoblast invasion and incomplete spiral artery remodeling lead to placental hypoperfusion, hypoxia, and oxidative stress; in stage 2, the hypoxic placenta releases anti-angiogenic and pro-inflammatory factors, including soluble fms-like tyrosine kinase-1 (sFlt-1) and soluble endoglin (sEng), which trigger systemic endothelial dysfunction and the maternal clinical syndrome. The review highlights the central role of angiogenic imbalance, immune dysregulation, and chronic inflammation in disease progression. Particular emphasis is placed on maternal risk factors such as primiparity, advanced maternal age, obesity, diabetes mellitus, chronic hypertension, multiple pregnancy, prior preeclampsia, genetic susceptibility, and epigenetic regulation. We also emphasize the contribution of microRNAs in relation to placental hypoxia, trophoblast invasion, angiogenesis, endothelial injury and microchimerism to the development of preeclampsia. The review also examines the role of T helper 1 (Th1)/Th2/Th17/regulatory T cells (Treg) imbalance and uterine natural killer cell dysfunction at the maternal–fetal interface. Improved understanding of these interconnected mechanisms may support earlier diagnosis, better risk stratification, and the development of targeted preventive and therapeutic strategies.

International Journal of Molecular Sciences doi: 10.3390/ijms27104280

Authors: Yang-Jin Shen Han-Fang Liu Ting-Chen Hsu Yi-Chieh Chen Yi-Chuan Cheng

Phospholipase A2 group VI (PLA2G6) regulates phospholipid remodeling and cellular homeostasis, and its mutations cause neurodegenerative disorders, including neurodegeneration with brain iron accumulation and PLA2G6-associated parkinsonism (PARK14). Although many cases present in adulthood, a substantial subset shows early onset, indicating that PLA2G6 dysfunction can affect neuronal systems during developmental stages. However, whether PLA2G6 directly regulates early neurogenesis remains undefined. Here, using zebrafish embryos, we investigated the role of Pla2g6 during neural development through loss- and gain-of-function approaches. pla2g6 is dynamically expressed during embryogenesis, with enrichment in the developing central nervous system during neurogenesis. CRISPR/Cas9-mediated Pla2g6 deficiency did not alter neural progenitor formation but significantly reduced neuronal precursors. Expression of the disease-associated PLA2G6 D331Y variant phenocopied this effect, confirming that the observed phenotype results from loss of Pla2g6 function. The reduction in neuronal precursors occurred without changes in proliferation but was accompanied by a marked increase in apoptosis, identifying neuronal precursor cell death as the primary mechanism. Under oxidative stress conditions, Pla2g6 overexpression reduced neuronal apoptosis, whereas Pla2g6 deficiency markedly enhanced reactive oxygen species -induced apoptosis. These findings establish Pla2g6 as a regulator of oxidative stress-associated apoptotic signaling during neurogenesis. Together, these results define Pla2g6 as a stage-specific determinant of neuronal precursor survival, linking lipid homeostasis and oxidative stress control to early neural development. This study establishes a developmental framework for PLA2G6-associated disorders and positions impaired neuronal precursor survival as a contributing mechanism underlying disease onset.

International Journal of Molecular Sciences doi: 10.3390/ijms27104279

Authors: Ki Hyun Nam

β-Glucosidase (BGL) is widely used in biofuel production, industrial value-added chemicals, and food industry applications. The substrate entrance loops of BGL play a role in substrate specificity and accessibility. To better understand the substrate entrance loops of BGL, a high-resolution crystal structure of BGL from Thermoanaerobacterium saccharolyticum (TsaBGL) was determined at 1.65 Å, and all-atom molecular dynamics (MD) simulations were performed. The crystal structure of TsaBGL exhibited both folded and straight conformations of the flexible L3 loop, along with rigid conformations of L1, L2, and L4 loops. MD simulations revealed that the folded L3 loop transitioned to a straight conformation, indicating the preference for the straight conformation. At the optimal temperature for enzyme activity, the flexibility of the L3 loop of TsaBGL decreased, whereas that of the L1 loop increased. Moreover, the positions of L1 and L2 loops shifted in a direction opposite to the substrate entrance, resulting in an expanded substrate-binding entrance and increased substrate accessibility to the active site. MD simulations of three homologous BGLs showed that, despite sequence variability, a conserved dynamic trend exists in which the L1 loop exhibits higher flexibility, whereas the L3–L4 loops maintain structural rigidity under optimal conditions. These results provide both an understanding of the loop dynamics involved in substrate accessibility in BGLs and insights into enzyme engineering to improve catalytic performance.

International Journal of Molecular Sciences doi: 10.3390/ijms27104278

Authors: Mariam M. Jaddah Samer N. Khalaf Mohammed Mukhles Ahmed Aisha Abdullah Alshanqiti

Spi-1 Proto-Oncogene (SPI1) encodes Purine-rich box 1 Transcription Factor (PU.1), a transcription factor of the ETS family that regulates hematopoietic lineage commitment and immune cell differentiation. Alteration of PU.1 dose or ETS domain integrity may interfere with transcriptional programs, which adds to hematopoietic dysregulation and leukemogenesis. Even though changes in SPI1 expression have been associated with acute myeloid leukemia (AML), the structural and regulatory effects of missense mutations at the PU.1 ETS domain have not been entirely studied, and targeting the PU.1 ETS domain by ligands is an area of computational analysis that should be further pursued. To computationally describe deleterious missense variants of SPI1 in terms of structural stability, evolutionary conservation, post-translational modification (PTM) context and interaction networks, and to measure ADMET-mediated molecular docking of cinnamic acid with the PU.1 ETS domain (8EQG) as a potential modulator. Missense nsSNPs were obtained through Ensembl and narrowed down by consensus prediction of pathogenicity (PredictSNP, combining SIFT, PolyPhen, SNAP and PhD-SNP and other tools). InterPro/UniProt was used for domain mapping. SWISS-MODEL was used to produce wild-type and mutant PU.1 versions, which were analyzed on the structural alignment and Cα–Cα displacement parameters in UCSF Chimera (v1.19). The estimation of stability change was carried out with I-Mutant and MUpro. Prediction of PTM sites was done using MusiteDeep and exploration of functional partners was done using STRING. Human, mouse and zebrafish orthologue conservation was measured by means of MAFFT alignment. GEPIA2 was used to compare the expression of SPI1 in AML (TCGA-LAML) and normal tissues (GTEx). AutoDock Vina (grid center 6, −2, −9 A; 20 × 20 × 20 A; 16 exhaustiveness) was used to prepare cinnamic acid and dock it into the PU.1 ETS domain (8EQG), with SwissDock being used for consistency checks. SwissADME and ADMETlab 2.0 were used to predict drug-likeness, pharmacokinetics, and toxicity. Nine missense mutations were routinely considered as deleterious with the majority of them being located in or near the ETS DNA-binding domain. Structural comparisons showed local perturbations of the structure and I189F and H211P yielded the greatest conformational changes between prioritized variants whereas other forms had minimal movements. A predominantly destabilizing trend was supported by stability prediction whereby V241G had the strongest destabilization signal with further destabilizations being predicted in I189F and R259C. PTM mapping revealed several potential regulatory residues (phosphorylation, acetylation, ubiquitination, and methylation), which indicated that there could be crosstalk between the sequence variation and the transcriptional regulation. The SPI1 was placed in a central hematopoietic transcriptional module (containing RUNX1, CEBP members, GATA1 and IRF factors) by the STRING network. The cross-species alignment showed that there was high conservation of a number of the mutation sites, which would support functional constraint at the ETS region. The expression analysis revealed that the level of SPI1 mRNA in AML was significantly elevated compared to normal tissues. Docking also indicated a slight and reproducible interaction of cinnamic acid with the ETS domain (top affinity −4.27 kcal/mol), with a solitary leading polar anchor and supportive hydrophobic interactions, which is akin to interaction between fragments. The ADMET profiling revealed the likelihood of success in the oral drug-likeness and low CYP inhibition liability, as well as signifying the presence of a possible hepatotoxicity signal that needs further confirmation through experiments. Comprehensive computational studies suggest that certain pathogenic variants of SPI1 missense defects, especially in the ETS domain, can result in loss of PU.1 structural stability and regulatory environment, which are in line with the disturbed hematopoietic regulation and AML-related dysregulation. Cinnamic acid demonstrates moderate yet reproducible binding to the PU.1 ETS domain and has an overall favorable developability profile, which indicates that it is better considered as a starting scaffold, as opposed to an active inhibitor. The results give a logical basis of focused biochemical validation and structure-directed optimization of ETS domain modulators in hematologic disease settings.

International Journal of Molecular Sciences doi: 10.3390/ijms27104277

Authors: Jae-In Eom Se-Min Kim Joo Young Lee Ji-Woo Kim Dae Yoon Kim Jae Kwon Lee Cheol-Ho Pan

Obesity is associated with excessive lipid deposition in adipose tissue and the liver, leading to systemic metabolic disturbances. In this study, we investigated the anti-obesity efficacy of Tisochrysis lutea (TL) powder, standardized to fucoxanthin (12.18 ± 0.21 mg/g DW) and docosahexaenoic acid (DHA) (16.03 ± 0.49 mg/g DW), in a high-fat diet (HFD)-induced obesity model in C57BL/6N mice. TL supplementation (50–150 mg/kg) over eight weeks significantly reduced body weight gain by up to 63.2%, total white adipose tissue mass by 53.4%, and liver weight by 38.2% compared to the HFD control, without affecting renal safety markers. Histological examination revealed smaller adipocytes and diminished hepatic steatosis in TL-treated groups. Serum triglycerides and leptin concentrations were significantly lowered by 38.5% and 70.1%, respectively, while HFD-induced elevations of ALT and AST were reduced by 61.7% and 38.6%, respectively. At the transcriptional level, TL downregulated adipogenic markers including PPARγ, C/EBPα, and SREBP-1c by 46~54%, as well as lipogenic regulators including FAS and ACC1 by up to 72%. Furthermore, TL treatment upregulated the mRNA levels of HSL and AMPK 2.3- and 2.1-fold, respectively, compared to the HFD control. These findings indicate that fucoxanthin- and DHA-enriched TL powder improves obesity-related metabolic alterations by modulating lipid storage and utilization pathways, supporting its development as a marine-derived functional ingredient for metabolic health management.

International Journal of Molecular Sciences doi: 10.3390/ijms27104276

Authors: Velmurugan Thavasi Nirmal Choradia Naoko Takebe Neal Naito Susan Yeyeodu Peter William Sadler Dean Hougen Sanchith Velmurugan Jordan P. Metcalf Donna L. Tyungu Thirumalai Venkatesan

Diagnostic latency limits time-sensitive care and early detection, and exhaled breath provides a rapid, repeatable window into metabolic and inflammatory chemistry. We review real-time breath sampling and analytical technologies and evaluate their readiness for clinical adoption, with emphasis on molecular pathways reflected in the breath volatilome and in exhaled breath condensate. Real-time mass spectrometry enables kinetic VOC profiling and targeted quantification, while humidity-aware sensors and wearable condensate platforms extend monitoring beyond the laboratory. Pathway-anchored interpretation links breath readouts to ketone handling, isoprenoid metabolism, nitric oxide signaling, lipid peroxidation, uremic nitrogen handling, and microbiome–host co-metabolism, but performance remains vulnerable to confounding, drift, and non-representative comparators. Translation requires standardized breath fraction control, traceable features, robust quality systems, and governed device algorithm stacks so that breath outputs inform decisions and outcomes.

International Journal of Molecular Sciences doi: 10.3390/ijms27104270

Authors: Ying Tian Jiaqi Zhou Xinyi Pei Feiran Liu Feiyang Diao

Premature ovarian insufficiency (POI) impairs fertility and health in reproductive-age women, with autoimmune factors contributing to 4–30% of cases. To investigate immune dysregulation in POI, we developed two mouse models using pZP3 induction: regular immune (RE-POI) and enhanced immune (EN-POI) cycles. The EN-POI model exhibited stable, irreversible ovarian dysfunction, including disrupted estrous cycles, hormonal changes (elevated FSH, decreased AMH, and estradiol), follicular depletion, and infertility. Immune profiling demonstrated consistent T-lymphocyte imbalance across both RE-POI and EN-POI model groups, characterized by expanded splenic CD4+ T cells, diminished regulatory T cells, elevated systemic inflammatory cytokines, and ovarian fibrosis. Proteomic comparison between the control and EN-POI groups identified 198 differentially expressed proteins, mainly enriched in immune and inflammatory pathways. Based on these differential proteins, subsequent network analysis further identified six key hub proteins, namely Mmp9, Isg15, Ikbke, Siglec1, Pf4, and Cdkn1b. This study establishes a stable autoimmune POI model, elucidates T-cell imbalance with cytokine storm and fibrosis, and identifies key molecules linking immune abnormalities to ovarian failure, offering new insights into POI research.

International Journal of Molecular Sciences doi: 10.3390/ijms27104275

Authors: Martina Šemeláková Terézia Hudáková Peter Solár Ján Šalagovič Jozef Židzik

Plant-derived bioactive compounds represent a major foundation of modern anticancer therapy and remain a prolific source of molecules with clinically relevant activity. This review provides an integrated classification of plant-derived anticancer compounds based on their clinical development status and predominant molecular mechanisms of action. Established chemotherapeutic agents, including taxanes, vinca alkaloids, and camptothecin derivatives, are distinguished from investigational phytochemicals such as polyphenols, flavonoids, terpenoids, and alkaloids that are under preclinical or clinical evaluation. These compounds target key hallmarks of cancer through modulation of microtubule dynamics, inhibition of topoisomerases, regulation of oncogenic signaling and epigenetic processes, and suppression of angiogenesis, invasion, and metastasis. Particular emphasis is placed on multitarget phytochemicals that interfere with PI3K/Akt, NF-κB, JAK/STAT, and MAPK pathways, induce apoptosis, and promote epigenetic reprogramming. In addition, major translational challenges, especially limited bioavailability, are discussed alongside advances in nano-enabled delivery systems designed to enhance therapeutic efficacy and reduce systemic toxicity. Collectively, this framework highlights the continuing relevance of plant-derived compounds in oncology and supports their rational integration into precision cancer therapy.

International Journal of Molecular Sciences doi: 10.3390/ijms27104268

Authors: Haiyu Yang Bingyou Luo Jingmin Mo Junhui Xie Jianwei Luo Kunying Yu Jianhua Wei Haiyi Zhong

To promote green chemistry and improve the utilization of plant resources, flavonoids from Dalbergia pinnata (Lour.) Prain were extracted in this study by combining NADES (natural deep eutectic solvents) with UAE (ultrasound-assisted extraction). Among the 13 synthesized NADES, choline chloride (ChCl)–urea (NADES-13) exhibited the highest extraction rate, outperforming traditional organic solvents. The optimal conditions determined by response surface methodology (RSM) were as follows: ChCl–urea molar ratio of 1:3, moisture content of 60%, liquid-to-material ratio of 28.5 mL/g, ultrasonic extraction time of 49 min, and temperature of 62 °C. Under these conditions, the extraction rate reached 117.95 ± 5.97 mg/g, a 73.5% improvement compared with 80% EtOH extraction. The comparison of the two algorithms showed that RSM (R = 0.9981, RMSE = 0.6570) had better fitting accuracy and prediction stability under small sample conditions than MLP (R = 0.9427, RMSE = 5.261) and RF (R = 0.9431, RMSE = 5.2442). DFT (density functional theory) analysis demonstrated that hydrogen bonds, Van der Waals forces, and cation–π interactions mediate the interaction between NADES-13 and flavonoids. Ultrasonic cavitation-induced cell wall damage and the hydrogen-bond network of NADES-13 were confirmed separately by SEM (scanning electron microscopy) and FTIR (Fourier transform infrared spectroscopy). In vitro experiments showed that the extract possessed concentration-dependent antioxidant activity and strong antibacterial activity, with an inhibition rate of 96.87 ± 5.09% against Escherichia coli at a concentration of 0.04 mg/mL. In this study, a “Smart Optimization–Molecular Mechanism–Activity Verification” green extraction system was developed, which offers an efficient and environmentally friendly strategy for extracting plant bioactive components and contributes to the progress of green chemistry.

International Journal of Molecular Sciences doi: 10.3390/ijms27104274

Authors: Yingdi Liao Lianna Zhao Youyang Zhu Sirong Ye Jinqing Huang Zhichao Niu Luoqing Zhang Na Lei Peixin Guo Yuhuan Xie

Traumatic brain injury (TBI), a major cause of persistent cognitive impairment (CI), increases the long-term risk of developing dementia, including Alzheimer’s disease (AD). To elucidate this association, we systematically reviewed fluid biomarkers linked to post-TBI cognitive outcomes. A comprehensive search of the PubMed, Embase, and Cochrane Library databases was performed. A total of 29 clinical studies were included, reporting on several biomarkers related to neural injury and repair, AD-like pathology, and inflammation. Among these, neurofilament light chain (NfL), ubiquitin C-terminal hydrolase L1, total tau, and glial fibrillary acidic protein (GFAP) were consistently associated with CI and brain atrophy across various TBI severities and stages. Notably, certain biomarkers assessed during the acute phase (within 7 days post-injury), such as brain-derived neurotrophic factor, neuron-specific enolase, and interleukin-1β, showed significant correlations with CI. In contrast, elevated levels of GFAP and NfL measured during the recovery phase (6 months to 8 years post-injury) were significantly associated with TBI-related CI (TBI-CI). The findings also highlighted that axonal injury, glial activation, neuroinflammation, neuronal damage, and degeneration drive TBI-CI, with tau pathology and synaptic dysfunction emerging as potential bridges from TBI to AD. This review underscores the critical temporal dynamics of fluid biomarkers in TBI-CI, revealing that stage-specific biomarker profiles mirror distinct underlying pathophysiological processes. Future longitudinal studies should focus on well-characterized patient subgroups, adopt standardized diagnostic criteria, and integrate fluid biomarkers with neuroimaging and genetic data.

International Journal of Molecular Sciences doi: 10.3390/ijms27104273

Authors: Ji-Seon Lee You-rin Kim Dogeon Yoon Ji Hye Park Tae-Keun Kim Eun-Kyoung Choi Jun Hur Ji-Eun Song

Preterm labor is a major cause of neonatal morbidity and mortality and is frequently driven by infection-associated inflammation that promotes premature uterine activation. In this study, we investigated the effects of adipose stem cell-derived extracellular vesicles (ASC-EVs) on macrophage-mediated inflammatory signaling in uterine smooth muscle cells (HUtSMCs). An in vitro model was established by treating HUtSMCs with conditioned media derived from LPS-stimulated RAW264.7 macrophages. Activation of signaling pathways was assessed by Western blotting and immunofluorescence, and functional responses were evaluated using calcium flux and collagen gel contraction assays. Conditioned media from LPS-stimulated macrophages induced robust activation of MAPK (ERK1/2 and JNK) and NF-κB signaling, accompanied by IκB degradation and nuclear translocation of phosphorylated p65, whereas ASC-EVs pretreatment significantly attenuated these responses and reduced the expression of pro-inflammatory cytokines, including IL-6, IL-8, and MCP-1. Furthermore, macrophage-conditioned media enhanced intracellular calcium flux and contractile activity in HUtSMCs, both of which were suppressed by ASC-EVs. Inhibition of TLR4 signaling in macrophages reduced the inflammatory potency of conditioned media, indicating a key upstream role of macrophage TLR4 activation. Collectively, these findings demonstrate that ASC-EVs suppress macrophage-mediated inflammatory activation and downstream contractile responses, suggesting their potential as a cell-free therapeutic strategy for preventing inflammation-associated preterm labor.

International Journal of Molecular Sciences doi: 10.3390/ijms27104272

Authors: Toshinori Hirai Kan Katayama

Mineralocorticoid receptor antagonists (MRAs) are the cornerstone of the management of heart failure and chronic kidney disease. A well-known adverse event, hyperkalemia, is associated with fatal arrhythmia and discontinuation of MRA. Our narrative review discusses the personalized treatment of MRAs, focusing on the pharmacological profile and drug–drug interactions to address safety concerns related to hyperkalemia. Clinicians should scrupulously monitor potassium levels, especially during dose titration, and review each patient’s medication list. Cytochrome P450 3A4 (CYP3A4) inhibitors are pharmacokinetic precipitators that interact with most MRAs, except spironolactone, and adversely affect the risk of hyperkalemia, although suggestive evidence is scarce. Potassium-elevating drugs synergistically increase serum potassium levels when co-administered with an MRA (e.g., renin-angiotensin aldosterone inhibitors, co-trimoxazole, non-steroidal anti-inflammatory drugs, calcineurin inhibitors, and β blockers). Additional approaches include correction of metabolic acidosis using sodium bicarbonate, potassium-lowering therapy using loop and thiazide diuretics, and sodium-glucose cotransporter 2 inhibitors. Novel potassium binders enable patients to receive the maximum-tolerated MRA with fewer gastrointestinal side effects. Individualized interventions for hyperkalemia risk are important in treatment using MRA.

International Journal of Molecular Sciences doi: 10.3390/ijms27104271

Authors: Alexis Hipólito García Juan Bautista De De Sanctis

Adjuvants play a crucial role in increasing vaccination efficacy. While aluminum salts have historically been the most common adjuvants, recent research has turned to new compounds with enhanced adjuvant properties and improved safety. Cutting-edge nanotechnology, leveraging nanoformulations and novel delivery systems, has enhanced efficacy while reducing adverse effects. Microparticles, emulsions, and immunostimulants are now essential tools due to their significant potential for vaccine production. Additionally, advanced drug delivery systems (DDSs) have been developed using sophisticated technologies to expedite and optimize drug and vaccine delivery to specific target sites, thereby maximizing therapeutic efficacy and minimizing systemic accumulation. The latest DDSs offer numerous advantages over conventional drug delivery systems, including heightened performance, precision, and efficiency. These DDSs, comprising nanomaterials or miniaturized devices, feature multifunctional components that are biocompatible and biodegradable, with high viscoelasticity, thereby extending their circulating half-life. This review aims to provide an in-depth and up-to-date overview of adjuvants and technological advancements in vaccine delivery systems.

International Journal of Molecular Sciences doi: 10.3390/ijms27104269

Authors: Koichi Yamaguchi Ryuichi Nakano Akiyo Nakano Rio Kishi Kai Saito Mako Watanabe Yuki Suzuki Ryuji Sakata Miho Ogawa Hisakazu Yano

Carbapenemase-producing Enterobacterales (CPE) is a global threat. IMP-6, a prevalent carbapenemase in western Japan, is mostly disseminated via CTX-M-2 extended-spectrum β-lactamase (ESBL) co-producing Enterobacterales. However, the existence and characteristics of Enterobacterales harboring blaIMP-6 without blaCTX-M-2 remain unclear. We analyzed the phenotypic and genetic characteristics of clinical blaIMP-6-harboring Enterobacterales isolates, focusing on those lacking blaCTX-M-2. Overall, 220 blaIMP-6-harboring isolates collected from 76 Japanese hospitals between 2014 and 2021 were characterized by antimicrobial susceptibility, presence of CTX-M-type ESBLs, plasmid incompatibility, plasmid transfer experiments, and genome sequencing and analysis. Among these, 203 co-harbored blaCTX-M-2 group, with 90% of them demonstrating high conjugation frequency and broad-spectrum resistance to β-lactams. Of the remaining 17 isolates, nine lacked blaCTX-M, while eight co-harbored blaCTX-M-1 group (n = 2) or blaCTX-M-9 group (n = 6). Eleven isolates carried nontransferable plasmids with genetic structures distinct from those of blaIMP-6 and blaCTX-M-2 co-encoding plasmids, including eight non-incompatibility N plasmids. Fifteen isolates carried only blaIMP-6-encoding plasmids; two carried plasmids with blaIMP-6 and blaCTX-M (blaCTX-M-27 or blaCTX-M-65). This novel study revealed that blaIMP-6 can exist without blaCTX-M-2 on diverse, often nontransferable plasmids, suggesting distinct, lower dissemination pathways compared to those of epidemic blaCTX-M-2 co-carrying plasmids and highlighting previously overlooked plasmids that necessitate close monitoring.

International Journal of Molecular Sciences doi: 10.3390/ijms27104267

Authors: Jiang Gao Hongrui Ren Xuanfu Wu Cunzhi Zou Bin He Wenqiang Ma

Heat stress (HS) has emerged as a major environmental stressor, inducing oxidative stress and hepatic steatosis and impairing production performance and health in laying hens, with limited evidence-based nutritional interventions available. This study investigated the hepatoprotective effects of dietary silibinin (SIL) against chronic HS. In a 10-week trial, 252 43-week-old Hy-Line Brown hens were exposed to daily HS (32 ± 1 °C, temperature–humidity index [THI] > 73) and fed either a basal diet or one supplemented with 100 mg/kg SIL. SIL significantly increased laying rate (p < 0.05) and improved albumen height, Haugh units, and shell strength by week 8 (p < 0.05). Histological analysis showed a 48% reduction in non-alcoholic fatty liver disease (NAFLD) activity score, with significantly decreased hepatic triglyceride content (p < 0.05); Oil Red O staining confirmed reduced lipid droplet accumulation. SIL restored redox balance by increasing plasma, hepatic total superoxide dismutase (T-SOD), and glutathione peroxidase (GSH-Px) (p < 0.05), increasing hepatic catalase (CAT) and glutathione (GSH) levels while decreasing malondialdehyde (MDA) (p < 0.05). Untargeted plasma metabolomics identified 11 key metabolites related to 2-oxoglutarate and purine metabolism, while hepatic transcriptomics revealed 835 differentially expressed genes primarily in the PPAR signaling and fatty acid biosynthesis pathways. SIL suppressed de novo lipogenesis via downregulation of ACACA and FASN, and enhanced β-oxidation through upregulation of CPT1A and ACSL1 (p < 0.05). Molecular docking indicated favorable binding affinities between SIL and these targets, which was further supported by corresponding changes in protein expression via Western blotting. Correlation analysis revealed a consistent alignment between the upregulation of ACSL1/CPT1A and improvement in performance and antioxidant status, suggesting a coordinated metabolic shift. These findings emphasize the potential of SIL as a sustainable animal nutrition antioxidant additive, which can alleviate HS-induced lipid disorders in the liver of laying hens. Importantly, these hepatoprotective effects were demonstrated exclusively under chronic heat stress conditions; further studies incorporating a normothermic baseline are required to distinguish stress-specific mitigation from general metabolic stimulation.

International Journal of Molecular Sciences doi: 10.3390/ijms27104266

Authors: Abdullah Md. Sheikh Shozo Yano Shatera Tabassum Jubo Bhuiya Atsushi Nagai

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by memory loss and cognitive decline. Its main pathological features are extracellular plaques composed of aggregated amyloid-β (Aβ) peptides and intracellular neurofibrillary tangles formed by hyperphosphorylated tau. The Aβ hypothesis proposes that Aβ accumulation is a key driver of AD, influencing tau pathology, neuroinflammation, and neurodegeneration. However, therapies that reduce Aβ have shown limited clinical benefits. This suggests that the mechanisms underlying peptide-mediated modulation of AD pathology are much more complex. Both Aβ and tau undergo various post-translational modifications (PTMs) that affect their structure, aggregation, and toxicity. In addition, these abnormal proteins are not efficiently cleared in AD, indicating dysfunction of the protein quality control (PQC) system that maintains proteostasis. Such abnormal PTMs and impaired PQC likely work together to drive disease progression, which may explain the limited success of Aβ-reduction therapies. In this review, we describe how major PTMs, including phosphorylation, ubiquitination, acetylation, glycosylation, and oxidation, regulate the pathological behavior of Aβ and tau. We also discuss the role of the PQC systems in the pathology of AD. We propose that dysregulation of PTMs and PQC constitutes a convergent mechanism underlying AD pathogenesis. Therapeutic strategies targeting these processes may provide more effective and sustained disease modification than approaches focused solely on Aβ reduction.

International Journal of Molecular Sciences doi: 10.3390/ijms27104265

Authors: Alexey Starshin Alexandr Mazur Nikolai Mugue Daria Kaplun Artemiy Golden Ekaterina Khrameeva Egor Prokhortchouk

Understanding the phenotypic consequences of epigenetic variation and its role in adaptation remains a central challenge in evolutionary biology. Marine and freshwater sticklebacks provide a powerful system to study the interplay between genetic and epigenetic components of phenotypic plasticity that enables colonization of contrasting salinity habitats. Here, we used whole-genome bisulfite sequencing (WGBS) to characterize DNA methylation entropy—a measure of epigenetic stochasticity—in gill tissue from marine and freshwater ecotypes. We found that freshwater sticklebacks exhibit elevated methylation entropy in divergence islands (DIs), genomic regions known as hotspots of genetic divergence between marine and freshwater populations. Within DIs, we identified a subset of genes exhibiting concurrent increases in methylation entropy and transcriptional variance, including osmoregulatory candidates involved in growth modulation, cytoskeletal reorganization, metabolism, and extracellular matrix remodeling. Their linked variability suggests that they may act as “adaptation capacitors” facilitating phenotypic plasticity during salinity transitions. Exploratory enrichment analysis further revealed overrepresented epigenetic regulators within DIs, such as DNA demethylase TET1 and chromatin remodelers ARID5B and BPTF, indicating a potential regulatory basis by which these factors may convert genetic variation into epigenetic diversity. Collectively, our findings demonstrate that DIs are focal points of both genetic divergence and epigenetic heterogeneity, consistent with a model in which DIs may act as multi-layered genomic regions associated with adaptive responses to salinity change.

International Journal of Molecular Sciences doi: 10.3390/ijms27104264

Authors: Karel Novák Kalifa Samaké

Infections in animal production industries can be reduced through targeted breeding of animals with genetically enhanced disease resistance. This type of breeding should be based on a thorough understanding of host defence and its underlying mechanisms. The genes controlling the components of the innate immune system represent a primary target. Their function is highly sensitive to any mutational changes in their structure, which has been optimised through long-term evolution. A source of variability is provided by the polymorphism in the genes encoding components of the Toll signalling pathway as one of the main subsystems of innate immunity. The associated set of genes comprises the group of TLR genes encoding the so-called Toll-like receptors (TLRs), as well as genes encoding other key components of the Toll signalling pathway. Specific attention is paid to the genes encoding the crucial interactors of Toll-like receptors, namely the adaptor MyD88 and other adaptors containing the TIR region. Due to the extremely high evolutionary conservation of this region, any structural variation is expected to have functional consequences on the organismal level. The study of the TLR adaptor MyD88, as well as other related adaptors, has been underestimated in farm animal species, as evidenced by the limited number of research outputs. However, this contrasts with the numerous published functional associations for these genes in human medicine. Such a disparity suggests that further research in this direction in farm animal species may yield novel and important findings in the future.

International Journal of Molecular Sciences doi: 10.3390/ijms27104263

Authors: Iwona Agnieszka Jabłońska Marcin Goławski Dorota Ścieglińska Urszula Kacorzyk Natalia Wojciuszkiewicz Tomasz Wojciech Rutkowski Agnieszka Maria Mazurek

The qualitative detection of circulating tumor human papillomavirus DNA (ctHPV) has shown promise in HPV-associated cancers. We performed a systematic review and meta-analysis to evaluate the association of pretreatment ctHPV levels with survival outcomes and quantitative tumor burden metrics. Databases were searched through 5 January 2026. Studies were eligible if they included patients with HPV-associated cancers and reported quantitative pretreatment ctHPV levels in relation to survival outcomes or tumor burden. Twenty-three studies were included in the quantitative synthesis. Higher pretreatment ctHPV levels were associated with poorer progression-free survival (PFS) (8 studies, n = 883; HR = 1.86, 95% CI 1.19–2.90; p = 0.013). This association was primarily driven by studies in oropharyngeal cancer (OPC; HR = 2.47, 95% CI 1.59–3.84; p = 0.007), whereas no significant association was observed in cervical cancer. In multivariable analyses, elevated ctHPV remained associated with shorter PFS (HR = 1.87, 95% CI 1.66–2.10; p = 0.002). No significant association was observed for overall survival. Pretreatment ctHPV correlated with nodal volume in OPC (r = 0.45), nodal and tumor volume in OPC/anal cancer (r = 0.39), primary tumor volume in OPC (r = 0.22), and tumor diameter in cervical cancer (r = 0.44). Higher pretreatment ctHPV levels are associated with greater tumor burden and poorer PFS in HPV-associated OPC. CtHPV shows potential as a prognostic biomarker, although further prospective studies and assay standardization are needed.

International Journal of Molecular Sciences doi: 10.3390/ijms27104261

Authors: Ekaterina Tikhonova Anna Popinako Aleksey Sazonov

Bst DNA polymerase is a biotechnologically modified thermostable enzyme from the thermophilic Gram-positive bacterium Geobacillus stearothermophilus. The unique structure of Bst DNA polymerase determines its thermal stability, ability to replace a DNA strand and specificity. The high specificity of Bst DNA polymerase ensures the efficiency, sensitivity, and high rate of loop-mediated isothermal amplification (LAMP), which is widely used in vitro biotechnology. The review reveals the structural and functional features of the enzyme, its application in LAMP and methods of improvement of thermal stability (including directed evolution, site-directed mutagenesis, fusion constructs, and chemical modifications). The terminal transferase activity and ab initio synthesis are discussed regarding problems of Bst DNA polymerase and the ways to eliminate them. The questions of introducing modified nucleotides and primers to expand the diagnostic capabilities of LAMP are also discussed. Modern advances in Bst DNA polymerase engineering pave the way for the creation of reliable, thermostable, and highly specific test systems suitable for widespread diagnostic applications.

International Journal of Molecular Sciences doi: 10.3390/ijms27104262

Authors: Antreas Ermogenous Eleni Sarigiannidou Maria Psomiadou Afroditi Panagiotidou Georgia Persephoni Voulgaridou Despoina Eugenia Kiousi Daniela Moyankova Dimitar Djilianov Alex Galanis Aglaia Pappa

The resurrection plant Haberlea rhodopensis is a rare species endemic to Greece and Bulgaria, renowned for its exceptional desiccation tolerance and rich phytochemical composition. This study investigated the antioxidant, cytoprotective, and wound-healing-associated effects of H. rhodopensis ethanolic extract (HEE) in human keratinocytes (HaCaT cells) under oxidative and cytotoxic stress conditions. Antioxidant capacity was initially evaluated using a plasmid DNA protection assay, in which HEE attenuated oxidative DNA damage induced by a Fenton reaction system and preserved the native supercoiled structure of pUC19 plasmid DNA. Cytotoxicity screening using the sulforhodamine B (SRB) assay and real-time proliferation monitoring (HoloMonitor® M4) identified 20 μg/mL as a non-toxic pre-treatment concentration (EC10). Under hydrogen peroxide (H2O2)-induced oxidative stress, HEE pre-treatment maintained cell viability and significantly reduced intracellular reactive oxygen species (ROS) levels, indicating a protective effect. In vitro wound-healing assays demonstrated enhanced scratch closure in keratinocyte monolayers. RT-qPCR analysis revealed modulation of antioxidant-related genes (CAT, SOD1, HMOX1, NQO1, GPX, GSR), while mRNA sequencing suggested selective stress-adaptive responses, involving extracellular matrix (ECM)-, metabolic-, and tissue-repair/aging-associated pathways. Overall, HEE exhibits antioxidant and cytoprotective effects in keratinocytes and is associated with transcriptional changes linked to cellular stress responses and wound closure. These findings support its potential relevance for dermatological, pharmaceutical, and cosmeceutical applications, while further studies are required to establish the underlying molecular mechanisms.

International Journal of Molecular Sciences doi: 10.3390/ijms27104260

Authors: Daniela Crescenti Irene Petracci Andrea Cesareni Giuliano Binetti Barbara Borroni Roberta Ghidoni

Psychiatric disorders, such as major depressive disorder (MDD), bipolar disorder (BD), and schizophrenia (SZ), comprise a heterogenous group of severe mental illnesses (SMIs) characterized by disturbances in cognition, emotional regulation, or behavior. Cognitive impairment represents an accompanying feature of many SMIs, often interfering with or limiting essential daily life activities. SMIs arise from a complex interplay of genetic, epigenetic, developmental, and environmental factors that disrupt neural and cellular processes. SMIs often present with overlapping symptoms and sometimes co-occur, making misdiagnosis a common clinical challenge. To date, there is a lack of reliable and specific biological markers to aid in the differential diagnosis of cognitive impairment in SMIs and for distinguishing neurodegenerative dementias from SMIs with overlapping symptoms. In this context, blood-based biomarkers of the ATX(N) system associated with cognitive deficits in neurodegenerative diseases, such as neurofilament light chain (NfL), glial fibrillary acidic protein (GFAP), amyloid beta (Aβ), and tau proteins, may help to understand the biological basis of cognitive dysfunction in SMIs and support differential diagnosis. This narrative review summarizes the current evidence on the application of blood-based biomarkers of neurodegenerative dementias in SMIs and their association with the cognitive deficits observed in these conditions, as well as their relevance for differential diagnosis, disease monitoring, and the evaluation of treatment efficacy in psychiatric disorders.

International Journal of Molecular Sciences doi: 10.3390/ijms27104259

Authors: Tanaporn Wangsanut Yin Htet Htet Aung Yin Htet Htet Oo Narin Lawan Monsicha Pongpom

Talaromyces marneffei is a dimorphic fungal pathogen that can subvert host immune defenses; however, the molecular mechanisms underlying its interactions with host cells remain incompletely understood. Glutathione peroxidase from T. marneffei (TmGpx1) has previously been identified as an antigenic protein that elicits antibody responses in patients with talaromycosis. To elucidate the contribution of TmGpx1 during human–fungal pathogen interaction, the yeast two-hybrid system was performed using TmGpx1 as bait to screen a cDNA library derived from non-induced human macrophage cells. Sixteen candidate host protein partners were identified, with Gene Ontology analysis revealing their predominant association with cytoskeletal and extracellular exosome components. To examine the atomic-level structural interface and dynamic behavior of protein–protein interactions, we employed molecular dynamics (MD) simulations to investigate the interaction between TmGpx1 and FKBP15, a human protein involved in early endosomal regulation and associated with both microtubule and actin filaments. Per-residue decomposition analysis using gmx_MMPBSA identified LEU124 of TmGpx1 and ARG616 of FKBP15 as critical residues mediating the protein–protein interaction. Notably, the key residues of TmGpx1 are located toward the N-terminus and are mapped outside of the catalytic active site, suggesting that the interaction of TmGpx1 with host cytoskeletal components may occur independently of its enzymatic antioxidant activity. Overall, our findings provide novel insights into the repertoire of host cytoskeletal and membrane trafficking proteins that may be targeted for remodeling during T. marneffei infection. Elucidation of these molecular interactions advances our understanding of host–pathogen dynamics and opens new avenues for the development of targeted diagnostics and therapeutic strategies against talaromycosis.

International Journal of Molecular Sciences doi: 10.3390/ijms27104258

Authors: Andrés J. Cortés

Climate-change-driven abiotic stresses, once regarded as episodic constraints for major staple crops, are now main selective forces driving the agronomic and evolutionary trajectories of plants [...]

International Journal of Molecular Sciences doi: 10.3390/ijms27104257

Authors: Zhili Tian Qinghua Yin Chenglong Zhou Xiaochu Wu Fei Liu Jun Li

Diabetic kidney disease (DKD) is a primary cause of end-stage renal disease (ESRD), and while ferroptosis is known to contribute to DKD pathogenesis, the regulatory role of the NLRP3 inflammasome in this process remains elusive. To address this research gap, we explored whether NLRP3 inhibition alleviates DKD by suppressing ferroptosis using streptozotocin-induced diabetic wild-type and NLRP3-knockout C57BL/6 mice, alongside high-glucose-cultured (30 mM) human renal tubular epithelial (HK-2) cells with or without siNLRP3 transfection. Inflammatory cytokines (IL-6, TNF-α, and IL-1β) were measured using an ELISA; oxidative stress markers (CSSG, MDA, GSH, and ROS) and the iron ion content via colorimetric assays; mitochondrial morphology by transmission electron microscopy (TEM); and ferroptosis-related proteins (ACSL4, COX2, and GPX4) through Western blotting. Our findings demonstrate that NLRP3-knockout diabetic mice displayed markedly reduced urinary albumin excretion and serum creatinine levels (p < 0.01) compared with wild-type diabetic controls, concurrent with suppressed renal iron overload and ferroptosis, diminished inflammatory cytokine levels, and attenuated oxidative stress. Pathological assessments further revealed ameliorated renal fibrosis and preserved mitochondrial ultrastructure in NLRP3-deficient mice. In vitro, siNLRP3 transfection abrogated high-glucose-induced inflammation, oxidative stress, and ferroptosis in HK-2 cells, effects that were reversed by the ferroptosis inducer erastin (p < 0.01). Mechanistically, NLRP3 deficiency was associated with upregulated GPX4 expression and downregulated ACSL4 and COX2 expression. Collectively, these results indicate that inhibition of the NLRP3 inflammasome mitigates DKD progression by suppressing ferroptosis, underscoring its translational potential as a therapeutic target for this condition.

International Journal of Molecular Sciences doi: 10.3390/ijms27104256

Authors: Sukrita Punyauppa-Path Nonthiwat Taesuk Sujira Maneerat Priyapa Najomtien Pongpat Kiatprasert Watchara Kanchanarach Nattawadee Kanpipit Srisan Phupaboon

Riceberry rice milk (RBRM) is rich in phytochemicals, particularly anthocyanins, which are known for their potential in managing type 2 diabetes (T2D). This study aimed to develop a novel RBRM-based yogurt derived from its polysaccharide and protein components and to evaluate the effects of supplementation with W. globosa powder (WGP) at 0% (F1, control), 5% (F2), 10% (F3), and 15% (F4) on nutritional and functional properties. Among all formulations, F4 exhibited the highest nutritional values, including dietary fiber (41.25%), curd protein (21.34%), and carbohydrate (starch) content (25.25%), with a lower fat content (2.13%) compared to other groups. In terms of antioxidant activity, F4 showed high total phenolic content (33.70 mg GAE/g) and total flavonoid content (25.2 mg QUE/g), along with strong radical scavenging activities, with DPPH and ABTS inhibition values of 41.52% and 78.18%, respectively. Furthermore, F4 demonstrated notable antidiabetic potential through α-amylase and α-glucosidase inhibition, with IC50 values of 0.89 and 1.32 mg/mL, respectively. Widely targeted metabolomics analysis identified 88 differential metabolites between F4 (potent condition) and F1 (control group). Twelve selected compounds from RBRM–WGP yogurt contributed to increased levels of amino acids, peptide derivatives, saccharides, organic acids, polyphenols, and flavonoids. Molecular docking analysis revealed that key metabolites, including vignatic acid B, glimepiride, and indoramin, exhibited strong binding affinities with the active sites of α-amylase (PDB: 2GVY, Aspergillus niger) and α-glucosidase (PDB: 3A4A, Saccharomyces cerevisiae). These findings indicate that phytonutrient compounds, particularly indoramin, play a significant role in enhancing the nutritional composition and functional properties of RBRM–WGP yogurt for potential applications in food processing.

International Journal of Molecular Sciences doi: 10.3390/ijms27104255

Authors: Xinpeng Yin Chenglin Hu Chenxue Yin Jiaying Li Chengcheng Wang Yupei Zhao

Pancreatic steatosis is closely associated with metabolic disorders, pancreatitis, and pancreatic cancer, yet the underlying mechanisms remain incompletely understood and ideal animal models are lacking. We established and compared four mouse models based on distinct pathogenic mechanisms. In the high-fat diet (HFD)-fed model, pancreatic steatosis occurred later than hepatic steatosis. In ob/ob mice, despite severe obesity and hepatic steatosis, no significant intrapancreatic fat deposition was observed. In the caerulein combined with HFD model, caerulein markedly accelerated HFD-induced intrapancreatic fat accumulation, indicating a synergistic effect of inflammation and metabolic stress. Orthotopic injection of adipogenically differentiated 3T3-L1 cells established a focal model without altering systemic metabolism, enabling investigation of localized fat deposition. Collectively, these four models recapitulate metabolic, genetic, inflammatory, and localized mechanisms, exhibit divergent histological features, and provide a complementary platform for mechanistic studies and drug screening in pancreatic steatosis.

International Journal of Molecular Sciences doi: 10.3390/ijms27104248

Authors: Cora Rebecca Schindler Dirk Henrich Lena Krämer Inna Schaible Jason-Alexander Hörauf Aileen Ritter Philipp Störmann Rald Victor Maria Groven Markus Huber-Lang Ingo Marzi Liudmila Leppik

Severe traumatic brain injury (TBI) is a leading cause of mortality and long-term disability in polytrauma (PT) patients, and its clinical outcome remains difficult to predict due to clinical heterogeneity and secondary injury mechanisms. Current diagnostic and prognostic approaches based on clinical assessment and imaging are limited, particularly in PT where neurological evaluation is often impaired. This study aimed to compare plasma- and extracellular vesicle (EV)-associated microRNA (miRNA) signatures in patients with severe TBI and healthy controls to identify their potential as minimally invasive biomarkers and to improve understanding of molecular responses. For profiling circulating miRNAs, blood samples were collected at ≤3 h and at 48 h after admission. In the screening phase, plasma samples of n = 15 patients with severe isolated TBI (Abbreviated Injury Scale [AIS]Head ≥ 4, all other AIS ≤ 1) and n = 15 age- and sex-matched healthy controls were pooled (n = 5/pool) and subjected to next-generation sequencing (NGS). In the following validation phase, n = 25 severely injured trauma patients (Injury Severity Score [ISS] ≥ 16) were enrolled and stratified into PT without TBI (PT; AISHead = 0; n = 13) and isolated TBI (n = 12). Differentially expressed candidate miRNAs identified in the screening phase were validated in individual plasma and EV samples using reverse transcription droplet digital polymerase chain reaction (RT-ddPCR). Functional enrichment and pathway analyses were performed using miRNet. NGS identified more differentially expressed miRNAs in plasma (ER: 103; 48 h: 65) than in EVs (Emergency Room [ER]: 14; 48 h: 32). Functional enrichment analysis indicated associations with pathways related to cellular stress, senescence, growth factor signaling, transcriptional regulation, and apoptosis. In validation, 12 of 16 plasma and 10 of 15 EV-miRNAs were confirmed as differentially expressed in TBI patients; among these, three plasma and four EV miRNAs differed between TBI and PT. After adjustment, most plasma miRNAs were associated with injury severity rather than group status. EV miRNA profiles showed heterogeneous patterns, with miR-1469 associated with TBI group status in adjusted analysis, while miR-1237-5p was linked to injury severity and other EV miRNAs showed no consistent group-specific effects. Plasma miRNAs mainly correlated with systemic injury markers, whereas EV miR-1469 showed a moderate association with the Glasgow Coma Scale (GCS). Overall, circulating miRNA profiles after injury appear to be predominantly influenced by systemic trauma severity rather than TBI-specific effects. Plasma miRNAs mainly reflected general injury burden, whereas EV-associated miRNAs showed more heterogeneous patterns, with miR-1469 emerging as a candidate associated with TBI after adjustment for clinical covariates. These findings suggest that EV-derived miRNAs, particularly miR-1469, may provide more targeted signals related to brain injury and warrant further investigation.