Biomolecules doi: 10.3390/biom16091255

Authors: Xiaojia Guo Yanzhe Huang Yinghan Hu Lingyun Zhang Zongbao K. Zhao

The ubiquitous nicotinamide adenine dinucleotide (NAD) engages in diverse biological processes, leading to non-selective energy transfer toward target synthetic reactions. To achieve selective energy transfer in complex biological systems, we previously constructed artificial systems mediated by the non-natural cofactor nicotinamide cytosine dinucleotide (NCD), which can be specifically recognized by engineered enzymes with minimal cross-talk with natural cofactors. For enhanced energy transfer and higher product yields, efficient conversion of NCD to NCDH is required to deliver reducing power in NCD-mediated biosynthetic pathways. Here, we established a comprehensive strategy for selective reduction in intracellular NCD. First, coupled enzymatic colorimetric assays with high specificity were validated for quantifying NAD, NADP, and NCD. With phosphite as the energy source, we selectively elevated the intracellular NCDH/NCD ratio with minimal perturbation to NADH/NAD and NADPH/NADP ratios in E. coli. To overcome the limitation of phosphite transmembrane transport, cell-free systems were constructed to confirm that phosphite could drive near-complete NCD reduction. Finally, cells were treated with polymyxin B, which promoted phosphite uptake and thereby enabled maximal reduction in intracellular NCD. An NCDH/NCD ratio of 47 was achieved, demonstrating that 98% of the intracellular NCD pool existed in the reduced form. This work demonstrates that NCD can function as an independent redox cofactor for selective regulation, providing viable strategies for artificial cofactor-driven biosynthesis.

Biomolecules doi: 10.3390/biom16091254

Authors: Pere Domingo Paula Prieto

The spectrum of diseases in individuals with human immunodeficiency virus (HIV) receiving successful antiretroviral therapy has evolved over time. In the past, they developed opportunistic infections and malignancies, whereas today, cardiovascular disease is among the most common causes of illness and premature death. Traditional risk factors for atherosclerosis (hypertension, hyperlipidemia, smoking, diabetes, family history of heart disease) are more prevalent in people with HIV than in the general population. However, it is well established that HIV itself causes increased immune activation, chronic inflammation, vascular dysfunction, and a cluster of metabolic abnormalities that contribute to a faster-than-usual rate of biological aging and a higher risk of developing atherosclerosis, a risk not fully captured by current risk models. In the REPRIEVE study, treatment with pitavastatin was shown to reduce the rate of first cardiovascular events among individuals with HIV receiving antiretroviral therapy. Importantly, the beneficial effects of statins on atherosclerosis likely extend beyond lowering cholesterol to include effects on vascular function and on immune and metabolic systems altered by HIV. Even among individuals on statins, a considerable risk of cardiovascular disease remains. Here, We provide a narrative review of current evidence and an expert perspective on emerging approaches to residual cardiovascular risk after REPRIEVE. We review the current understanding of atherosclerosis pathogenesis in individuals with HIV, focusing on recent findings from the REPRIEVE trial. We outline current approaches to improving cardiovascular risk assessment across clinical, biological, and computational levels. We also examine a growing number of therapeutic options that address residual inflammation and atherogenic metabolic disturbance in individuals with HIV on long-term, effective antiretroviral therapy. Significantly, after REPRIEVE, we must move from prescribing statins to all individuals with HIV toward more individualized cardiovascular disease prevention strategies, integrating clinical information, a variety of biomarkers, imaging studies, and even molecular information to generate optimal individualized cardiovascular disease prevention regimens that reflect the complexity of this outcome in naturally diverse individuals.

Biomolecules doi: 10.3390/biom16091253

Authors: Keyu Guo Xiaofang Chen Chenyin Wang Yaru Liu Chao Liu Yexiang Wu Xiuyong Fan Yanni Xu Shuyi Si Yongxin Zhang Jing Zhang

Rising drug resistance undermines current anti-influenza virus therapies. Although targeting the hemagglutinin (HA)–sialic acid receptor interaction is a promising strategy, progress is impeded by the lack of subtype-independent screening models. Herein, we established a fluorescence-based cell high-throughput model using fluorescein isothiocyanate-conjugated Sambucus Nigra Lectin (FITC-SNA) as a stable HA surrogate and α-2,6-sialyltransferase (ST6GAL1)-overexpressing MDCK cells to mimic the HA–receptor interface. This platform was designed to serve as an efficient primary screening tool to rapidly filter large compound libraries for potential binders to the receptor-binding interface. Screening 10,000 compounds identified Obatoclax Mesylate and Ethylparaben as primary hits. Both exhibited broad-spectrum HA inhibition activity, validating the model’s capability to identify compounds interfering with viral attachment. Further cellular antiviral assays revealed cytotoxicity for both compounds, resulting in low selectivity indexes (SIs), indicating that while these molecules effectively target the interaction site, they require substantial structural optimization for therapeutic use. Molecular docking confirmed their binding to type A H1N1, H3N2, and B/Victoria HA proteins, while ADMET predictions highlighted specific structural optimization needs to mitigate toxicity. In conclusion, this subtype-independent, highly specific high-throughput screening (HTS) model provides an efficient and reliable platform for early-stage influenza drug discovery and lead compound development.

Biomolecules doi: 10.3390/biom16091252

Authors: Youyou Zheng Kent A. Lee Unimunkh Uriyanghai Christine Wai Mihaela Mocanu Anthony Z. Yang Huanjuan Su Lianxia Li Vinay A. Sudarsanam John S. Poulton Prabir Roy-Chaudhury Gang Xi

Uremic conditions are common in end-stage kidney disease (ESKD) patients. Accelerated vascular diseases in uremic patients lead to heart failure, stroke, and hypertension. To investigate the effects of uremia on porcine arterial smooth muscle cells (aSMCs), bulk RNA sequencing was used to identify uremia-induced alterations in signaling pathways of aSMCs that might explain the aggressive cardiovascular diseases seen in patients with chronic kidney disease (CKD) and ESKD. Bulk RNA sequencing was performed on porcine aSMCs cultured with serum from normal or uremic pigs. Differentially expressed gene (DEG) analysis revealed that 295 genes were upregulated and 138 genes were downregulated after uremic serum exposure. Gene Ontology molecular function analysis demonstrated that ATP-dependent activity, translation factor activity, and ATP-dependent protein folding chaperones were predicted to be negatively enriched after uremic serum exposure, while proton transmembrane transporter activity, antioxidant activity, and glutathione peroxidase activity were predicted to be positively enriched. Gene set enrichment analysis indicated that the cell cycle was predicted to be negatively enriched after uremic serum exposure in aSMCs. Overrepresentation analysis found that focal adhesion, protein processing in the endoplasmic reticulum (ER) and cell senescence were predicted to be negatively enriched, while lysosome, phagosome, apoptosis, and autophagy were predicted to be positively enriched after uremic serum exposure. This study suggests that the signaling pathways that regulate cellular redox homeostasis, the cellular waste disposal system, ER stress and autophagy are major signaling pathways involved in aSMCs’ responses to uremic serum exposure. These pathways may contribute to the severe arterial-specific clinical symptoms observed in CKD/ESKD patients, such as arterial stiffness, vascular calcification and cardiovascular disease.

Biomolecules doi: 10.3390/biom16091251

Authors: Noa Fine-Shamir Avital Beig Arik Dahan

Developing effective oral formulations for poorly soluble anticancer drugs remains a major pharmaceutical challenge due to the combined limitations of solubility, permeability, and efflux transporter activity. In this work, we investigated the influence of the nonionic surfactants Cremophor EL, Pluronic P-85, and Pluronic F-68 on the solubility and intestinal permeability of the anticancer drug etoposide. All surfactants significantly increased etoposide aqueous solubility. While in vitro permeability across an artificial membrane demonstrated the expected solubility-permeability tradeoff, in vivo SPIP studies in rats revealed a distinctive solubility-permeability interplay for Cremophor EL and Pluronic P-85, which simultaneously enhanced solubility and permeability, likely through P-gp inhibition. In contrast, Pluronic F-68 exhibited the classical solubility-permeability tradeoff, consistent with its reported negligible P-gp inhibitory activity. Mechanistic analysis indicated that surfactant hydrophobicity and molecular weight critically influence P-gp inhibition via ATPase modulation. Surfactants with higher hydrophobicity and moderate molecular weight can integrate into the phospholipid bilayer, enabling direct interaction with P-gp and disruption of its ATPase function. These findings provide strategic insights for the rational design of oral formulations capable of overcoming the solubility-permeability tradeoff, improving the bioavailability of challenging anticancer drugs, and may facilitate the transition from intravenous to oral chemotherapy.

Biomolecules doi: 10.3390/biom16091250

Authors: Baojian Yu Zekai Shao Zhuona Ni Yuxin Gao Ziyang Ding Weifeng Jiang Lin Li Lisheng Chu

The neurovascular unit (NVU) is composed of a diverse array of cells and an extracellular matrix (ECM). Neural cells and blood vessels are intricately interconnected, forming a cohesive whole. Specific cellular components and structures within the NVU play an indispensable role in maintaining homeostasis of the central nervous system (CNS). With the advancement and maturation of cell co-culture technology, various three-dimensional (3D) NVU models continue to emerge, offering a more objective and comprehensive perspective for in vitro studies of CNS diseases. Specifically, these 3D NVU models include Transwell Chamber models, gel-PDNS-based 3D models, self-assembled NVU models and microfluidic NVU models, which reconstruct the complex NVU architecture to varying degrees. This review systematically summarizes multiple 3D construction strategies for in vitro NVU to overcome the limitations of conventional cellular tests or animal experiments, highlights the critical roles of biomimetic gel in recapitulating native cell-gel crosstalk, comparatively analyzes four major 3D NVU technical routes in terms of cellular composition, vascular morphology, barrier performance, and reproducibility, categorizes application scenarios of 3D NVU platforms oriented to practical research demands, including oxygen-glucose deprivation/reoxygenation (OGD/R) injury modeling, BBB permeability assay, CNS drug penetration screening, neuroinflammation and neurotoxicity evaluation, proposes practical principles for model selection under different experimental purposes, and concludes with current bottlenecks, including imperfect vascular network maturation and lack of unified evaluation criteria, together with future perspectives for standardized 3D NVU in vitro. By comparing the advantages and limitations of these approaches, we aim to clarify their optimal applicability for investigating specific pathological mechanisms and screening potential therapeutics.

Biomolecules doi: 10.3390/biom16091249

Authors: Yuwei Ge Qianqian Wang Yuying Fu Tingting Wang Huajun Liao Chongchong Yan

Potato (Solanum tuberosum L.) seedlings are highly sensitive to freezing temperatures, which severely impairs growth and causes substantial losses in tuber yield and quality. This study aimed to screen freezing-tolerant potato germplasm accessions, identify candidate genes involved in the freezing response, and provide elite parental materials and a theoretical reference for molecular breeding of freezing-tolerant cultivars. We evaluated seedling freezing tolerance of 73 potato accessions using the freezing damage index (FDI), and performed transcriptome sequencing on leaf samples from highly freezing-tolerant (HT) accession 15-1881 and highly freezing-susceptible (HS) accession B8 following freezing treatment. Substantial variation in freezing tolerance was observed across the germplasm panel, with 5 HT accessions and 12 HS accessions identified, showing marked phenotypic and physiological differences under freezing stress. Transcriptomic analysis detected 6560 differentially expressed genes (DEGs) in 15-1881 and 5161 DEGs in B8, with 3558 DEGs specific to 15-1881. The phenylpropanoid biosynthesis pathway exhibited noticeable expression divergence between 15-1881 and B8, harboring 17 15-1881-specific DEGs including three tandem phenylalanine ammonia-lyase (PAL) genes. The HT germplasm accessions obtained in this study provide breeding resources for freezing-tolerant potato improvement, and the PAL genes characterized here represent promising candidate genes associated with freezing response in potato.

Biomolecules doi: 10.3390/biom16091248

Authors: Amelia T. Y. Yam Yuek Ling Chai Saima Hilal Cai Yuan Vincent C. T. Mok Narayanaswamy Venketasubramanian Boon Yeow Tan Ming Ann Sim Mitchell K. P. Lai Christopher P. Chen Joyce R. Chong

Dysregulated insulin signaling in the brain has been linked to cognitive impairment and dementia. Insulin-like growth factor 1 (IGF-1) is a peptide growth hormone crucial for neurogenesis and neuroprotection. Findings regarding potential involvement of IGF-1 in dementia have been conflicting, and the status of IGF-1 in clinical cohorts with Alzheimer’s disease (AD) and concomitant cerebrovascular disease (CeVD) burden is unknown. A Singapore-based memory clinic cohort consisting of 46 non-cognitively impaired (NCI), 101 with cognitive impairment, no dementia (CIND) and 81 AD dementia subjects underwent plasma IGF-1 measurements and neuroimaging assessments for association analyses of peripheral IGF-1 with regional brain volumes, as well as with neuroimaging CeVD markers (lacunes, cerebral microbleeds, white matter hyperintensities). Plasma IGF-1 levels were significantly lower in AD compared to NCI and CIND participants (both p < 0.001). Plasma IGF-1 was significantly associated with smaller hippocampal (p = 0.035), amygdala (p = 0.024), parietal lobe (p = 0.029), and frontal lobe (p = 0.002) volumes. In contrast, plasma IGF-1 did not associate with CeVD markers after covariate adjustments. Our findings suggest that plasma IGF-1 may be a blood-based biomarker for reduced brain volumes, while having no direct role in CeVD pathophysiology.

Biomolecules doi: 10.3390/biom16091247

Authors: Dániel Vörösvácki Nikolett Szakállas Alexandra Kalmár István Takács Béla Molnár

Transposable elements (TEs) account for nearly half of the human genome and shape chromatin organization, gene regulation, and genome evolution. However, their contributions to human physiology and disease remain incompletely understood. The most active elements in humans, LINE-1 (L1), Alu, and SVA, retain some copies with the ability to evade epigenetic repression and mobilize via target-primed reverse transcription (TPRT), whereas copies become inactive through various fragmentations and mutations. TE activity contributes to genomic instability and has been implicated in aging, cancer, neurological disorders, chromatin organization, and epigenetic regulation. Studying TE is challenging due to their repetitive and polymorphic nature. Recent advances in sequencing technologies and short- and long-read sequencing platforms, combined with specialized bioinformatic pipelines, currently enable more comprehensive characterization of TE insertions, deletions, expression, and epigenetic status. Computational approaches vary in sensitivity, specificity, and resource requirements, and their performance is influenced by sequencing modality, coverage, and the reference genome used. Assembly-based and read-based methods, as well as integrating methylation data or single-cell data, provide complementary insights into TE biology. This review summarizes the biology of active human TE, surveys state-of-the-art short- and long-read pipelines for TE analysis, and highlights their applications in studies of aging, cancer, and other complex diseases. We also provide practical guidance for selecting appropriate sequencing strategies and tools for TE-focused projects, and discuss emerging approaches and open questions in the field.

Biomolecules doi: 10.3390/biom16091246

Authors: Ratan K. Chaudhuri Raja K. Sivamani

Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disease characterized by epidermal barrier dysfunction, immune dysregulation, microbial imbalance, and severe pruritus. Emerging evidence establishes that barrier disruption is a central pathogenic driver capable of initiating inflammatory signaling, neuroimmune activation, and chronic disease instability. This understanding has shifted therapeutic paradigms toward barrier-directed strategies aimed at restoring epidermal resilience. This narrative review evaluates the mechanistic and clinical evidence surrounding isosorbide fatty acid diester molecules—specifically isosorbide dicaprylate (IDC) and isosorbide di-(linoleate/oleate) (IDL)—as a barrier-first approach for AD management. Early in vitro and ex vivo investigations demonstrated that IDC significantly improves epidermal hydration, transepidermal water loss, and the expression of barrier-associated genes linked to epidermal integrity. Subsequent studies showed that IDL expands these effects through coordinated regulation of keratinocyte differentiation, lipid homeostasis, and inflammatory stress pathways. Furthermore, recent mechanistic data highlight synergistic anti-inflammatory and pruritus-modulating effects involving TRPA1-, TRPV3-, and TSLP-associated pathways, while preserving tissue integrity under cytokine-induced stress. Clinically, these findings are supported by randomized studies in pediatric and adult cohorts demonstrating significant reductions in pruritus, favorable Eczema Area and Severity Index (EASI) responses, decreased topical corticosteroid dependence, and a reduction in the relative abundance of Staphylococcus aureus. Collectively, these findings support a barrier-first therapeutic framework in which restoration of epidermal resilience may beneficially influence multiple interconnected pathways involved in atopic dermatitis.

Biomolecules doi: 10.3390/biom16091245

Authors: Ayesha Jabeen Ilaria Barison Honoria Ocagli Bruna Fata Diego Perazzolo Cristina Basso Roberto Luisetto Silvia Pozzo Fabrizio Mancin Enrico Grisan Dario Gregori Annalisa Angelini Marny Fedrigo Chiara Castellani

Background: Heart failure remains a leading cause of morbidity and mortality, and current therapies rarely repair established myocardial damage. Nanoparticle-based interventions have been investigated across heterogeneous models of myocardial injury, remodeling, cardiomyopathy, and heart failure, but the distribution and translational maturity of this evidence remain unclear. Methods: A systematic search of PubMed, Embase, Scopus, and Web of Science was conducted from database inception to June 2024. Eligible reports were mapped according to disease model, experimental system, carrier-level nanoparticle platform, payload, route, comparator, outcomes, biodistribution, safety assessment, and translational characteristics. Reports of non-therapeutic nanoparticle exposure were retained in a separate contextual safety/toxicology stratum and were not included in the therapeutic evidence-density map. Risk of bias was evaluated using design-appropriate tools. Results: Of 2640 records screened, 157 independent studies met the criteria: 140 in the main therapeutic/platform evidence map and 17 in a separate contextual safety/toxicology stratum. Within the main corpus, polymeric systems were the largest platform class (n = 50), followed by inorganic/mineral (n = 35), biological/biomimetic (n = 24), lipid-based (n = 23), carbon-based (n = 5), and hybrid/multicomponent systems (n = 3). Evidence was concentrated in acute myocardial injury (n = 76), while direct same-agent comparisons, long-term safety assessment, repeated dosing, quantitative biodistribution, and clinically aligned heart-failure models remained limited. Conclusions: The field demonstrates substantial formulation diversity and biological activity, but translation is constrained by fragmented characterization, sparse comparative evidence, and incomplete assessment of biological fate and safety.

Biomolecules doi: 10.3390/biom16091244

Authors: Jessica Costa Andrea Atrei Juan José Valle-Delgado Monika Österberg Rebecca Pogni

Laccases are multicopper oxidases capable of oxidizing a wide range of substrates using molecular oxygen as the terminal electron acceptor, producing water as the sole by-product. High-redox potential fungal laccases, such as those from Trametes versicolor, are particularly attractive for industrial and environmental applications, although their use is often limited by sensitivity to operational conditions. Enzyme immobilization represents an effective strategy to enhance laccase stability and reusability. In this work, magnetic nanoparticles (MNPs) were investigated as support for laccase immobilization due to their high surface area, biocompatibility, and ease of magnetic recovery. Two modified co-precipitation synthetic routes were systematically evaluated, and the size, morphology, and chemical composition of the products were characterized by microscopy, light scattering, and spectroscopic methods, while both adsorption and covalent immobilization strategies were explored. The MNP surface was found to be highly reactive toward radical species generated during laccase-catalyzed reactions, especially in the presence of small Fe2+ excess. While this can enhance the enzyme catalytic activity, it challenges the inertness of the support and promotes, in some cases, strong interactions between reaction products and the nanoparticle surface. These findings highlight a previously unexplored role of magnetic supports in laccase-based biocatalytic systems.

Biomolecules doi: 10.3390/biom16091243

Authors: Rachid Anane Su Melser Elodie Renouf Rachid Ennamany Jean-Michel Mérillon

Hibiscus plant cell cultures were developed to produce a cosmetic ingredient with anti-ageing properties. UHPLC-DAD-MS analysis of Hibiscus plant cell cultures revealed a high content of polyphenols, particularly hydroxycinnamic acid derivatives, including caffeoyl and p-coumaroyl conjugates. The biological activity of a 50/50 mixture of extracts from Hibiscus syriacus and Hibiscus rosa-sinensis cells was investigated in a human keratinocyte/fibroblast co-culture model, which better reproduces the reciprocal epithelial–mesenchymal interactions between epidermal keratinocytes and dermal fibroblasts than monocultures, using quantitative data-independent acquisition (DIA) LC-MS/MS proteomics combined with functional enrichment and protein–protein interaction analyses. A total of 7062 proteins were identified, of which 280 were differentially expressed (107 upregulated and 171 downregulated) following hibiscus treatment. The proteomic profile suggested coordinated molecular reprogramming associated with extracellular matrix remodelling, tissue repair, hydration, and attenuation of inflammatory signalling. Functional enrichment analysis revealed coordinated modulation of extracellular matrix organization, glycosaminoglycan metabolism, lysosomal function, cell communication, and inflammatory signalling. Upregulation of extracellular matrix and adhesion proteins, including lumican, collagen VIII, fibulin-5, syndecans, and glypicans, suggested coordinated extracellular matrix remodelling that may promote skin firmness and elasticity, while the downregulation of inflammatory regulators, including CARD16 and S100 family proteins, suggested attenuation of innate inflammatory responses. Overall, these findings provide mechanistic insights into the biological activity of Hibiscus cell culture extracts and support their potential as cosmetic ingredients promoting skin homeostasis and healthy skin ageing.

Biomolecules doi: 10.3390/biom16091242

Authors: Gennady N. Chuev Timur V. Mamedov Dmitry O. Morozov

Hydration plays an essential role in protein–protein interactions. Coarse-grained modeling provides an efficient way to treat hydrated protein complexes without the use of extra-large computational resources. To enhance the capabilities of coarse-grained modeling, we developed an integral equation theory based on the solution of the Ornstein–Zerinke equation to evaluate the hydration structure of peptides and proteins within the framework of coarse-grained modeling. Our current version is based on the SPICA force field, which considers distance-dependent interaction potentials between solvent particles and amino acid segments. Our approach involves two key procedures: an accurate estimation of the structure factor of the uniform fluid and the specific construction of bridge functions obtained from MD simulations. The use of a special hybrid closure allows us to reproduce not only the details of the structure factor, but also the isothermal compressibility obtained from the simulations. The developed bridge functions include two components: an analytical repulsive contribution, which is primarily responsible for the thermodynamic properties, and an attractive contribution obtained from MD simulations. The main assumption in the construction is that the contribution of individual amino acids to the attractive bridge function is additive. By parameterizing the bridge functions, we reproduced details of the hydration structure and accurately calculated the hydration energy for various peptides and proteins. Our method is computationally inexpensive and appears to be suitable for the rapid processing of hydrated proteins of any size.

Biomolecules doi: 10.3390/biom16091241

Authors: Aodi Fan Xinwei Chen Ke Yang Xuefang Ma Haohao Gao Binyan Wang Guanwei Fan Lan Li

The heart–kidney axis has emerged as a central framework for understanding the bidirectional interactions that drive cardiorenal syndrome and broader cardiovascular–kidney–metabolic (CKM) disease. However, existing interpretations have often emphasized hemodynamic and neurohormonal mechanisms without fully integrating the growing evidence for endocrine, inflammatory, and metabolic mediators that coordinate injury across organs. This Review was therefore undertaken to provide an updated and clinically relevant synthesis of the physiological basis of heart–kidney communication, the mechanisms underlying its disruption, and the therapeutic implications of these insights. To achieve this aim, we performed a systematic narrative review of the literature using PubMed, Embase, Web of Science, and Scopus for studies, supplemented by manual screening of reference lists. Priority was given to original studies, large cohort analyses, randomized controlled trials, meta-analyses, and authoritative reviews. We integrated evidence spanning physiological regulation, maladaptive signaling pathways, emerging mediators, experimental models, and evolving treatment strategies. The reviewed evidence indicates that heart–kidney crosstalk is driven not only by altered perfusion and venous congestion, but also by sustained activation of the renin–angiotensin–aldosterone system (RAAS) and sympathetic nervous system (SNS), inflammation, oxidative stress, mitochondrial dysfunction, anemia, uremic toxins, and disordered mineral metabolism. Among novel mediators, fibroblast growth factor 23 (FGF23) emerges as a major bone-derived, chronic kidney disease (CKD)-associated endocrine mediator linking renal injury to cardiac hypertrophy, fibrosis, calcium mishandling, and diastolic dysfunction, whereas Klotho appears to exert counter-regulatory protective effects. Heart-derived natriuretic peptides, including atrial natriuretic peptide (ANP) and B-type natriuretic peptide (BNP), remain important modulators of renal blood flow, natriuresis, and volume homeostasis. We further highlight the translational relevance of newer biomarkers and therapies, including sodium–glucose cotransporter 2 inhibitors (SGLT2is), glucagon-like peptide-1 receptor agonists (GLP-1 receptor agonists), and mineralocorticoid receptor antagonists (MRAs), which may help address cardiac and renal dysfunction in parallel. Overall, this Review supports a revised conceptual model in which the heart–kidney axis is governed by multidirectional hemodynamic, neurohormonal, immune, and endocrine signaling networks. A more integrated understanding of these mechanisms may improve biomarker discovery, refine risk stratification, and promote therapies that target both organs simultaneously.

Biomolecules doi: 10.3390/biom16091240

Authors: Bence György Gombás Erika Gábor Viktor Honti Orsolya Németh-Szatmári Ferenc Jankovics Zoltán Villányi

Assemblysomes are ribosome-nascent chain condensates that regulate co-translational processes through liquid–liquid phase separation, yet the sequence determinants underlying their formation remain incompletely understood. Previous studies identified the DNA helicase Sgs1 as an assemblysome-associated protein; however, whether its N-terminal region possesses intrinsic phase separation propensity has not been experimentally examined. Here, we investigated the first 135 amino acids of Sgs1 using a light-inducible optoDroplet assay. A mCherry–Cry2–Sgs11–135 fusion construct was compared with the established positive control FUS–mCherry–Cry2 and the negative control mCherry–Cry2 in live HEK293T cells. Following blue-light activation, Sgs11–135 reproducibly formed reversible condensates, indicating intrinsic phase separation propensity. Quantitative image analysis revealed light-dependent increases in condensate number, average condensate area, and integrated condensate fluorescence intensity. Compared with FUS, Sgs11–135 formed slightly fewer and smaller condensates but displayed reproducible light-dependent condensate formation. These findings indicate that the Sgs1 N-terminal region exhibits intrinsic phase separation propensity in a validated optogenetic assay. Although this proof-of-principle study does not establish the molecular mechanism of assemblysome formation, the results are consistent with the hypothesis that the Sgs1 N-terminus may contribute to the multivalent interactions underlying assemblysome organization.

Biomolecules doi: 10.3390/biom16091239

Authors: Qiaohua Li Shaoxuan Liu Jingxing Gao Jie Li Hong Shi

Primary human epidermal melanocytes are valuable models for pigmentation research, but maintaining prolonged expansion together with stable melanocytic characteristics can be challenging. Here, primary melanocytes were transduced with an hTERT-overexpression lentiviral vector to generate a mixed population (MIX) and three single-cell-derived clones (SC1, SC3, and SC4). RNA sequencing was performed on passage-6 primary melanocytes, MIX cells, SC clones, and three melanoma cell lines (A375, WM-115, and SK-MEL-1). hTERT overexpression extended melanocyte culture lifespan by more than 10 passages. TERT expression increased in MIX cells and was highest in SC clones. Principal component and gene-expression analyses showed that MIX and SC cells remained globally closer to primary melanocytes than to melanoma cell lines, without an evident melanoma-like transcriptomic shift. However, lifespan extension and clonal selection were accompanied by marked morphological changes and broad transcriptional remodeling involving cell-cycle regulation, telomere-associated processes, antiviral responses, extracellular matrix organization, adhesion, dendrite-related programs, and pigmentation. Melanocyte differentiation and pigmentation programs were generally reduced, particularly in clonal cultures. These findings support hTERT-extended melanocytes as expandable in vitro models, while highlighting that hTERT expression and single-cell cloning can induce functional model drift.

Biomolecules doi: 10.3390/biom16091238

Authors: Shuying Fu Yuhuan Meng Keying Liang Meiying Feng

Skeletal muscle regeneration depends on coordinated transitions of muscle stem cells (MuSCs), also known as satellite cells, from quiescence through activation and proliferative expansion to differentiation and fusion, while self-renewal replenishes the quiescent MuSC pool within a dynamically remodeled niche. Fibroblast growth factor (FGF) signaling regulates these transitions, but its effects vary as MuSCs and their niche change across regenerative stages. FGF output is shaped by ligand availability and extracellular presentation, fibroblast growth factor receptor (FGFR) isoform expression and coreceptor availability, receptor trafficking, intracellular feedback, and the state of the responding cell. Following acute injury, FGF inputs can support MuSC activation and expansion; signaling is subsequently reconfigured during differentiation, fusion, self-renewal, and return to quiescence. Aging-associated regenerative decline, chronic injury and dystrophic remodeling, denervation, and metabolic dysfunction disrupt this coordination and can uncouple FGF activity from productive repair. Rhabdomyosarcoma provides a distinct malignant context in which the FGF network is rewired to sustain oncogenic myogenic cell states. Here, we integrate molecular, cellular, and niche-level evidence across these settings to explain why FGF signaling produces divergent outcomes and to clarify how cellular context and timing should inform therapeutic modulation.

Biomolecules doi: 10.3390/biom16091236

Authors: Omer Unal Nilufer Akgun-Unal

Diabetes mellitus (DM) is a chronic metabolic disease characterized by hyperglycemia, and the diaphragm—the primary respiratory muscle—is adversely affected by this diabetic process. The aim of this study is to investigate the effects of zinc sulfate (ZnSO4) treatment on diaphragm muscle contractile dynamics, calcium homeostasis, apoptosis, and fibrosis in an 18-month-old female Type 2 diabetic rat model. Thirty-two 18-month-old female Wistar rats were randomly divided into four groups: Control (CON), CON + ZnSO4, Diabetes Mellitus (DM), and DM + ZnSO4. The DM model was induced by a high-fat diet and administration of 30 mg/kg streptozotocin (STZ); after the disease was confirmed, ZnSO4 was administered intraperitoneally at a daily dose of 10 mg/kg to the treatment groups. The mechanical functions of the diaphragm muscle were evaluated using a post-rest potentiation protocol in an isolated organ bath; qPCR analyses (Caspase-3, TGF-β1, SERCA2a) were performed to investigate cellular apoptosis, fibrosis, and calcium regulation. Compared with the CON group, the DM group exhibited a severe ~90% reduction in diaphragmatic contraction force (CF) and a ~97% decline in maximal contraction/relaxation velocities (±dF/dtmax) (p < 0.0001), which strongly correlated with a 30% suppression of SERCA2a gene expression (p < 0.01). Concomitantly, apoptotic Caspase-3 (~2.6-fold) and profibrotic TGF-β1 (~3.1-fold) mRNA levels were significantly elevated (p < 0.0001). In the DM + ZnSO4 group, daily zinc treatment (10 mg/kg/day, i.p. for 6 weeks, initiated 4 weeks after diabetes confirmation) did not reverse the elevated Caspase-3 and TGF-β1 expressions (p > 0.05). However, SERCA2a expression was fully preserved back to control levels (p < 0.05 vs. DM), leading to a substantial ~3-fold improvement in CF and velocities (p < 0.05 to p < 0.0001 vs. DM). On the other hand, the healthy CON + ZnSO4 group exhibited a physiological slowing of contractility (~53% decrease in CF), without histological damage, likely due to a competitive antagonism between excess divalent zinc (Zn2+) and calcium (Ca2+) on myofilaments. Although zinc cannot reverse the structural apoptotic and fibrotic remodeling in the aged diabetic diaphragm, it successfully rescues functional contractility by preserving SERCA2a transcriptional expression.

Biomolecules doi: 10.3390/biom16091237

Authors: Shijin Lan Ying Wang Yutong Fu Shixing Yang Quan Shen Xiaochun Wang Wen Zhang Deqiang Wang Likai Ji

Tripartite motif-containing protein 21 (TRIM21/Ro52) is a pivotal E3 ubiquitin ligase and cytoplasmic fragment crystallizable receptor (FcR). It plays a crucial role in viral infections, autoimmune disorders, and cancers by regulating multiple cell signaling axes, including the NF-κB, RIG-I-like receptor (RLR), cGAS-STING, and Toll-like receptor (TLR) pathways. Type I interferon (IFN-I), a pleiotropic cytokine, is produced via these immune signaling pathways, which are often triggered by viral components. TRIM21 both activates IFN-I signaling and mediates its negative feedback through post-translational modification of key immune signaling proteins, thereby maintaining immune homeostasis. In recent years, TRIM21 has been found to dually regulate autophagy and IFN-I in the context of virus–host interplay. Herein, we systematically summarize the functional roles of TRIM21 in virus-triggered intracellular immunity, aiming to provide insights for researchers and inspire further investigation in this area.

Biomolecules doi: 10.3390/biom16091235

Authors: Diana Culej Bošnjak Doris Janjić Petra Korać Mariastefania Antica Maja Matulić

The urokinase plasminogen activator or urokinase is a highly specific extracellular protease involved in numerous physiological and pathological processes. Its activity is a consequence of its interplay with its inhibitor, PAI1, and receptor, uPAR, and is finely regulated at several levels. The aim of the work was to investigate whether endoplasmic reticulum stress can modulate urokinase activity. Two tumor cell lines grown in cell culture were treated with Thapsigargin and sodium salicylate, inducers of ER stress response. Urokinase activity was determined in the conditioned media, and expression of uPA system molecules and molecules involved in response to ER stress in cell lysates was measured. ER stress influenced urokinase activity: while in the glioblastoma line its activity was increased, in breast cancer cells it was decreased. Differences in activity were a consequence of urokinase and PAI1 expression at the protein and RNA level. However, ER stress decreased cell migration, invasion, and proliferation regardless of the changes in urokinase activity. Gene expression analysis indicated that cell specific activation of some transcription factors and pathways could be responsible for different urokinase activity regulation.

Biomolecules doi: 10.3390/biom16091234

Authors: Mariarosaria De Rosa Theresa M. Heidenreich Libby Childs Benura Azeroglu Sneh M. Toprani Nader Aryamanesh Pablo Galaviz Hilda A. Pickett Eros Lazzerini Denchi Zachary D. Nagel Patricia L. Opresko

Telomeres are highly susceptible to oxidative DNA damage, particularly 8-oxoguanine (8-oxoG), which is processed by glycosylase-initiated base excision repair (BER). OGG1 removes 8-oxoG opposite C, and MUTYH removes A misinserted opposite 8-oxoG to prevent mutations. While OGG1 has an established role in telomere protection, the contribution of MUTYH to telomere stability in cancer cells after oxidative DNA damage remains poorly understood. Using a chemoptogenetic system to induce targeted 8-oxoG lesions specifically at telomeres in HeLa cancer cells, we demonstrate that MUTYH is required to prevent telomere shortening, telomere loss, and genomic instability after chronic damage. Yet, telomere damage in MUTYH-deficient cells does not cause sustained DNA damage signaling or reduced cellular proliferation. Whole-genome sequencing further reveals enrichment of G to T transversions within telomeric repeats in MUTYH-deficient cells, consistent with increased mutagenesis due to unrepaired 8-oxoG:A mispairs. Combined loss of MUTYH and OGG1 rescues damage-induced telomere aberrations and genomic instability, implicating BER-generated single-strand break (SSB) intermediates as major contributors to telomere instability. In agreement, exo-FISH and S1-END-seq analyses reveal that repair-proficient cells rapidly accumulate SSB intermediates after damage, which are later resolved, whereas glycosylase-deficient cells exhibit SSBs at later time points. Together, these findings identify MUTYH as a critical guardian of telomere integrity during chronic oxidative stress and provide insight into how defective BER at telomeres contributes to genomic instability in cancer cells, with implications for cancers associated with MUTYH deficiency and mutations.

Biomolecules doi: 10.3390/biom16091233

Authors: Yanxin Wang Zhenhao Zhao Tongyu Li Guoqi Liu Jiale Wang Zhoukun Li

β-1,6-Glucan is a functionally crucial polysaccharide of the fungal cell wall, although typically less abundant than β-1,3-glucan and chitin, its content, chain length, and branching vary considerably among species. Structurally, it serves as a covalent cross-linker tethering the external mannoprotein layer to the internal β-1,3-glucan-chitin network, contributing to cell wall integrity and plasticity. Biosynthetically, unlike chitin and β-1,3-glucan, which are synthesized by the plasma membrane-associated synthases, β-1,6-glucan biosynthesis depends on a multi-protein cooperative network spanning the endoplasmic reticulum (ER), Golgi, and cell surface, whose core catalytic machinery remains incompletely defined. Genetic and in vitro reconstitution studies have begun to delineate the contributions of ER-resident proteins (Kre5, Big1, Cwh41/Gls1, Rot2/Gls2, and Cne1), Golgi-localized Kre6/Skn1 family members, and cell-surface components (Kre9, Knh1, Kre1, and Kre11). Functionally, its biological roles are established by two complementary lines of evidence, namely enzymatic digestion by endogenous or exogenous β-1,6-glucanases and inactivation of the biosynthetic machinery. Collectively, these studies show that β-1,6-glucan is essential for cell wall architecture, GPI-anchored protein localization, fungal growth, morphogenesis, and virulence, and acts as a potent immunomodulatory molecule at the fungus–host interface. Elucidating its structure, biosynthesis, and function will advance fungal cell wall biology.

Biomolecules doi: 10.3390/biom16091232

Authors: Ching-Chieh Lin Yi-Chou Hou Po-Jen Hsiao Kuo-Cheng Lu

Bone remodeling is rhythmically regulated, yet the contribution of the circadian–melatonin axis to osteoporosis remains incompletely defined, in part because mechanistic findings obtained at high experimental concentrations are frequently extrapolated to physiological signaling. This narrative review examines that inference. PubMed/MEDLINE, Embase, Scopus, and Web of Science were searched from inception to July 2026 for English-language studies of melatonin, circadian clock genes, and bone; molecular, preclinical, epidemiological, and clinical evidence was appraised with attention to receptor dependence, exposure concentration, and study architecture. In osteoblast-lineage cells, melatonin promotes osteogenic differentiation through MT2-linked Wnt/β-catenin and MEK1/2–MEK5 signaling, post-translational stabilization of SP7, and modulation of the OPG/RANKL axis. By contrast, direct antiosteoclastic and antioxidant effects are usually reported at micromolar concentrations, four to six orders of magnitude above nocturnal plasma levels, and are increasingly attributable to receptor-independent chemistry converging on the ROS–KEAP1–NRF2 node shared with structurally unrelated antioxidant compounds. This exposure mismatch suggests that conventional oral doses engage receptor-mediated osteoblast pathways rather than reproduce high-dose antiresorptive effects; sustained exposure at or above 1 µM is not attainable by conventional oral administration, and the chronic safety of the doses that would be required has not been characterized. In humans, bone resorption has an intrinsic circadian rhythm, and night-shift work is associated with adverse skeletal outcomes, although causality remains unresolved. The five available randomized trials are small and heterogeneous; none was powered for fracture prevention, and none compared administration times for a skeletal endpoint. Melatonin therefore cannot currently be recommended for the treatment of osteoporosis. Human bone and marrow pharmacokinetics, receptor-specific in vivo dose–response experiments, and adequately powered monotherapy trials in established primary osteoporosis are the studies that would change this assessment.

Biomolecules doi: 10.3390/biom16091231

Authors: Eunjeong Lee Blaine Hunter Gordon Jasmina S. Redzic Anthony J. Saviola Sean P. Maroney Steven Shaw Mila Cordero Shaun Bevers Angelo D’Alessandro Kirk C. Hansen Sarah E. Clark Elan Eisenmesser

Sortase A (SrtA) enzymes covalently anchor surface proteins to Gram-positive bacterial cell walls, promoting colonization and virulence. In Streptococcus pneumoniae, previous studies identified both a domain-swapped dimer and an active refolded monomer, but the active enzyme has not been characterized at the structural and residue-specific level. Here, we performed quantitative proteomic comparisons of wild-type and SrtA knockout strains that confirmed the loss of multiple LPxTG-containing virulence factors, including ZmpB, NanA, and IgA1 protease, consistent with an essential role for SrtA in surface protein anchoring. To enable mechanistic studies, we established a biochemical framework to produce monomeric Streptococcus pneumoniae SrtA by refolding and developed a gel-based assay using recombinant substrates to monitor catalytic activity. The refolded monomer, but not the swapped dimer, catalyzed cleavage and transpeptidation of a canonical LPxTG substrate in a metal-independent manner under the conditions examined. We further report high-resolution NMR backbone assignments for the active monomer and identify substrate-induced chemical shift perturbations that localize to the active site. Together, these findings provide an integrated proteomic, biochemical, and NMR characterization of monomeric, catalytically active Streptococcus pneumoniae SrtA and reveal residue-specific interactions with a canonical LPNTG recognition peptide.

Biomolecules doi: 10.3390/biom16091230

Authors: Agnieszka Pałucha-Poniewiera

The use of animal models to study mental illnesses, such as depression, requires proper standardization and extensive expertise. Achieving good construct, face, and predictive validity in depression models is quite challenging. Currently, only a few environmental models, mostly based on chronic stress, and a limited number of genetic models fulfill these criteria. In the quest for new antidepressants, initial screening tests are employed as a preliminary step in research. While these tests do not always meet the requirements of a disease model, they are useful for the early identification of substances that may have antidepressant potential, paving the way for further studies based on established models. This approach to discovering antidepressants was originally designed for traditional medications, which typically act by modulating serotonergic, noradrenergic, and dopaminergic systems, and require multi-week administration to produce a therapeutic effect. In contrast, the new antidepressant ketamine offers rapid therapeutic effects following a single dose and exhibits distinctive behavioral outcomes in both screening tests and animal depression models. These effects have inspired a new model for the search for rapid-acting ketamine-like antidepressants. This review presents the behavioral effects of ketamine and discusses the methodologies used in the search for novel rapid-acting antidepressant drugs (RAADs).

Biomolecules doi: 10.3390/biom16091229

Authors: Assia Azouaghe Florence Back Walid Daoudi Abdelmalik El Aatiaoui Céline Spack Diana Potes Vecini David Hoogewijs

Photodynamic therapy (PDT) exploits photoactivated materials that generate reactive oxygen species (ROS) to induce selective cancer cell death. Nitrogen-doped carbon dots (N-CDs) have emerged as promising photosensitizers owing to their favorable optical properties, while hybridization with titanium dioxide (TiO2) may further enhance photoinduced ROS generation through improved charge separation. Here, we synthesized a series of N-CD/TiO2 hybrid composites with varying TiO2 content using a hydrothermal approach and systematically investigated the relationship between their physicochemical characteristics and biological activity. The hybrid materials were characterized by Fourier-transform infrared spectroscopy, X-ray diffraction, scanning electron microscopy, dynamic light scattering, and UV–visible spectroscopy. Among the formulations investigated, the composite containing 90% N-CDs and 10% TiO2 (N-CDs10T) exhibited the smallest hydrodynamic diameter, a relatively narrow particle size distribution, favorable optical properties, and the strongest irradiation-dependent biological responses. Biological activity was evaluated in A549 lung adenocarcinoma and Kelly neuroblastoma cells. Under dark conditions, all formulations displayed relatively low intrinsic cytotoxicity. Following irradiation with 365 nm UVA light, however, N-CDs10T induced a marked increase in intracellular ROS production, activation of antioxidant response element (ARE)-dependent signaling, disruption of cell-cycle progression, apoptosis-associated cell death, and inhibition of cell proliferation and migration. Kelly cells exhibited greater sensitivity than A549 cells, with IC50 values decreasing from 0.98 mg/mL under dark conditions to 0.52 mg/mL following irradiation. Collectively, these findings demonstrate that N-CD/TiO2 hybrid composites function as photoresponsive materials that enhance ROS-mediated cytotoxicity upon light activation. Beyond demonstrating phototoxicity, this study systematically links hybrid composition with oxidative stress signaling and multiple cellular responses, providing a comprehensive biological evaluation of N-CD/TiO2 hybrid materials. While additional studies are required to identify the predominant ROS, evaluate selectivity in non-malignant cells, and optimize activation at clinically relevant wavelengths, the present work establishes a proof of concept for the development of N-CD/TiO2 hybrid composites for photodynamic applications.

Biomolecules doi: 10.3390/biom16091228

Authors: Joanna M. Shepherd Lucy R. Gibb Hew D. T. Torrance Joanna Manson Daniel J. Pennington Paul Vulliamy Karim Brohi

The cellular immune response underlying post-injury multiple organ dysfunction syndrome (MODS) remains incompletely described. We hypothesized that early perturbations in innate lymphocyte behavior are critical to the development of MODS in trauma patients. To address this, we examined lymphocyte subsets in a prospective cohort of major trauma patients recruited at a single major trauma hospital. Circulating lymphocytes were profiled with flow cytometry in serial samples drawn within the hyperacute (≤2 h) and acute (24 h, 72 h) post-injury periods. Plasma levels of specific mediators derived from innate lymphocytes were also measured in a larger cohort. We observed a marked hyperacute increase in circulating NK (particularly the CD56dim subset) and Vδ1 cells that were associated with MODS or early mortality. Absolute counts of NK activation markers CD69 and NKG2D were also higher in patients with adverse outcomes, although the proportion of NK cells expressing NKG2D was reduced. Exploratory cluster analyses of NK activating and inhibiting receptors identified patient groups with differing injury characteristics and outcomes. In plasma, patients who developed MODS had significantly higher levels of NK-associated cytotoxic mediators and cytokines. Collectively, these data indicate a specific pattern of hyperacute NK cell activation after major trauma that is characterized by a pattern consistent with cytotoxic lymphocyte activation and is associated with clinical outcome.

Biomolecules doi: 10.3390/biom16091227

Authors: Yue-Lin Fang Yu-Jou Hsu Chao-Hsien Sung Chia-Chi Kung Shiuan-Ruei Shiu Chih-Yu Hung Mei-Jung Chen Der-Chen Chang I-Chia Liang Chi-Feng Hung

Background: Age-related macular degeneration (AMD) is a leading cause of irreversible vision loss and is strongly driven by oxidative stress and inflammation. This study investigated the protective effects of cynarin against sodium iodate (NaIO3)-induced retinal pigment epithelium (RPE) injury, focusing on the MAPK and NF-κB signaling pathways. Materials and Methods: Human ARPE-19 cells were exposed to NaIO3, and cell viability was assessed by the MTT assay. Protein expression of MAPK components (p38, JNK, ERK) and the NF-κB pathway was analyzed by Western blotting, and pro-inflammatory cytokine (IL-1β, IL-6, TNF-α) mRNA expression was measured by RT-qPCR. In vivo, NaIO3-induced retinal degeneration in C57BL/6 mice was treated with cynarin (3 or 10 mg/kg) for seven days, and retinal changes were evaluated by fundus photography, fluorescein angiography, and OCT. Results: Cynarin preserved ARPE-19 cell viability without cytotoxicity. It significantly attenuated NaIO3-induced p38 and JNK phosphorylation, IκB degradation, and NF-κB activation while downregulating IL-1β, IL-6, and TNF-α expression. In vivo, cynarin reduced drusen-like lesions, hyperfluorescent abnormalities, and retinal thinning, and dose-dependently suppressed ocular pro-inflammatory cytokines. Conclusions: Cynarin protects against oxidative stress-induced retinal degeneration by suppressing MAPK and NF-κB inflammatory signaling, representing a promising therapeutic candidate for preventing or delaying NaIO3-induced dry AMD-like retinal injury.

Biomolecules doi: 10.3390/biom16091226

Authors: Zhishan Xu Dingbo Song Fangqi Hu Qiuhan Liang Mengyao Zhang Chao Lei Jinyuan Li Haiyi Guo Zhongbin Deng Zishan Yang

Inflammatory bowel disease (IBD) and colorectal cancer (CRC) are heterogeneous intestinal disorders that pose significant threats to human health and share common pathological features, including intestinal mucosal barrier disruption and gut microbiota dysbiosis, in which fucosylation acts as a critical regulatory mediator. Fucosylation is a highly conserved post-translational glycosylation modification involving the enzymatic transfer of fucose residues to glycoproteins and glycolipids. This tightly regulated process plays essential roles in maintaining intestinal homeostasis, mediating host–microbiota interactions and regulating immune responses. This review adopts a physiology-to-pathology framework, delineating fucosylation’s operational principles in healthy intestines and its dysregulation in IBD and CRC. It summarizes the spatial distribution of fucosylation, its regulatory mechanisms, and its roles in disease pathogenesis, and also discusses its potential as a diagnostic biomarker and therapeutic target. Finally, this review highlights future research directions to bridge mechanistic insights with clinical translation, emphasizing the promise of fucosylation in the precision diagnosis and treatment of intestinal disorders.

Biomolecules doi: 10.3390/biom16091225

Authors: Zhen-Zhen Dong Wanying Zheng Shuojie Lv Ling Peng Yihan Wang Qingjing Wang

Depression (major depressive disorder, MDD) is a globally prevalent, highly disabling, and complex mental disorder whose pathogenesis has not been fully elucidated. In recent years, the role of the gut microbiota in depression via the “microbiota–gut–brain axis” (MGB axis) has attracted increasing attention. A large body of evidence indicates that the gut microbiota and its metabolites can engage in bidirectional communication with the central nervous system through three core pathways—neural, immune, and metabolic—thereby profoundly influencing the onset and progression of depression. This article reviews the specific mechanisms by which the gut microbiota affects depression through the aforementioned pathways, including regulating the balance of neurotransmitters (e.g., GABA and 5-HT), mediating neuroinflammatory responses, and adjusting the levels of metabolites such as short-chain fatty acids. This study aims to provide a theoretical basis for an in-depth understanding of the pathophysiological mechanisms of depression and the development of novel microbiota-based intervention therapeutic strategies.

Biomolecules doi: 10.3390/biom16091224

Authors: Thanawat Pattananandecha Sutasinee Apichai Chalermpong Saenjum Young-Joon Surh

Bone remodeling is a dynamic and tightly regulated process that maintains skeletal homeostasis through a balance between bone formation by osteoblasts and bone resorption by osteoclasts. Disruption of this balance contributes to the development of bone-related disorders, particularly osteopenia, osteoporosis and osteogenesis imperfecta, which weaken, deform, or cause fractures. Increasing evidence indicates that oxidative stress and chronic inflammation impair osteoblast functions while promoting osteoclast differentiation and activity. Heme oxygenase-1 (HO-1) is a stress-inducible enzyme with cytoprotective, antioxidant, and anti-inflammatory properties. Besides its primary role in cellular defense against oxidative stress and inflammatory damage, HO-1 has been shown to be involved in both osteoblast differentiation and osteoclastogenesis. Through its interaction with key regulatory systems, including the receptor activator of nuclear factor κB (RANK)–receptor activator of nuclear factor κB ligand (RANKL)–osteoprotegerin axis and redox-sensitive signaling pathways, HO-1 contributes to maintenance of optimal bone remodeling. The enzyme also plays a role in modulating metabolic processes in the bone. This review highlights the role of HO-1 in bone formation, bone resorption, and related pathophysiologic conditions. Furthermore, the therapeutic potential of HO-1 as a target for bone disorders is discussed.

Biomolecules doi: 10.3390/biom16091223

Authors: He Zang Xinrui Chen Xiang Li Xue Yang Qingwei Tan Dafu Chen Rui Guo Jianfeng Qiu

Chalkbrood disease caused by Ascosphaera apis threatens honey bee brood, yet the transcriptional mechanisms that coordinate antifungal immune responses in Apis cerana remain unclear. Here, RNA interference (RNAi) was used to examine two Dorsal homologs and selected dorsal1 transcript isoforms during larval infection. A. apis inoculation increased dorsal1, dorsal2, and five antimicrobial peptide (AMP) transcripts in larval midguts, consistent with an infection-associated humoral response. Gene-level RNAi produced selective transcript responses: dorsal1 knockdown was accompanied by reduced apidaecin and defensin1 expression, whereas dorsal2 knockdown was accompanied principally by reduced defensin1 expression. abaecin, defensin2, and hymenoptaecin transcripts were not significantly altered after dorsal knockdown under the tested conditions. Isoform-targeted RNAi of RNA9886, RNA9888, and RNA9890 was likewise associated with distinct AMP transcript responses, with RNA9888 and RNA9890 more closely associated with defensin1. These transcript-level data support selective and partially overlapping Dorsal-associated regulation during the A. cerana larval response to A. apis, while direct differences in Dorsal protein abundance or activity remain to be established.

Biomolecules doi: 10.3390/biom16091222

Authors: Paul M. Harrison

In proteins, tracts compositionally biased by a subset of amino acids are often linked to intrinsic disorder. Such compositionally biased regions (CBRs) are sometimes analyzed for ‘sequence complexity’ (‘information entropy’) despite being an unlikely substrate for natural selection per se, and therefore not functionally implicated. Here, an algorithmic strategy applying compositional bias detection was designed to capture the wide diversity of CBRs in structured protein domains (termed ‘sCBRs’), ranging from trihomopeptides to >200 residues, with conservation and partner binding as functional lenses. sCBRs are common, with about 1/4th of domains harbouring them, but domains dominated by sCBRs over >50% of their lengths are rare (~1 in 200). Despite general assumptions, very short sCBRs are highly significantly sequence-conserved, and associated with ligand binding, even when common nucleotide/phosphate-binding or glycine-rich cases are disregarded. However, regardless of length, ~50% of cases are evolutionarily dynamic, undergoing clade-specific expansion/contraction. Protein-binding associations include aversions for short (≤16 residues) valine-rich regions in protein interfaces, and enrichments of longer alanine-rich cases (>16 residues). Only ~5% of cases are (at least partly) in intrinsically disordered loops, and are significantly shorter than sCBRs generally. Functional implications of sCBRs are discussed with many examples. The sCBR data might help with hypothesis generation and protein design/engineering.

Biomolecules doi: 10.3390/biom16091221

Authors: Rashmi Kumariya Carole A. Bewley

Human immunodeficiency virus (HIV) is an enveloped virus with a remarkable capacity for genetic diversification, enabling rapid escape from host immune responses and therapeutic interventions. Despite extensive global efforts, the development of an effective vaccine has remained elusive owing to the virus’s high genetic variability and antigenic diversity. Consequently, considerable effort has been directed toward the development of therapeutic agents targeting viral entry, reverse transcriptase, integrase, protease, and more recently, capsid. Although antiretroviral therapy (ART) remains the cornerstone of HIV treatment, it is associated with challenges including drug resistance, adverse side effects, and limitations in access and affordability. Targeting viral entry offers distinct advantages by blocking infection at the earliest stage of the viral life cycle and enabling the neutralization of free virions, as well as Fc-mediated elimination of HIV-infected cells in some cases. This review highlights promising protein-based HIV entry inhibitors that have demonstrated efficacy in preclinical studies, and discusses ongoing efforts to optimize their valency, avidity, specificity, serum half-life, effector functions, and production platforms to improve their therapeutic potential and economic feasibility.

Biomolecules doi: 10.3390/biom16081220

Authors: Sergeja Adamič Zamljen Sara Godena Nikola Major Smiljana Goreta Ban Tvrtko Karlo Kovačević Marija Polić Pasković Igor Pasković

Olive leaves represent a metabolically active tissue that plays an important role in plant responses to biotic stress. The present study comprised two independent experiments investigating biochemical responses of olive leaves to bacterial and fungal challenge under controlled conditions. Changes in primary metabolites (sugars, organic acids and free amino acids), phenolic compounds and lipid peroxidation were analyzed using chromatographic and spectrophotometric methods. In the bacterial experiment, pronounced differences were observed in primary metabolism. Tryptophan concentrations ranged from approximately 50 mg kg−1 DW to more than 360 mg kg−1 DW in ‘Istarska bjelica’, while sucrose concentrations reached up to 87 g kg−1 DW, demonstrating cultivar-dependent differences in carbohydrate metabolism. Phenolic profiling showed that secoiridoids were the dominant phenolic class, with oleuropein concentrations exceeding 27 g kg−1 DW across bacterial treatments. In the fungal experiment, amino acids showed greater variability than sugars and phenolic compounds, whereas MDA concentrations ranged from approximately 190 to 300 nmol g−1 DW but did not differ significantly among pathogen treatments. Overall, the two experiments showed distinct patterns of metabolite variation associated with bacterial and fungal challenge. These findings contribute to a better understanding of cultivar-dependent metabolic responses and provide a basis for future studies of olive–microbe interactions.

Biomolecules doi: 10.3390/biom16081219

Authors: Yakov Rabinovich Yoav Vardizer Shirley Pincovich Marva Wolowelsky Sofia Kulyamzin Miriam Ehrenberg Shiri Zayit-Soudry Inbal Man Peles Rina Leibu Nitza Goldenberg-Cohen Tamar Ben-Yosef

Microphthalmia, anophthalmia and ocular coloboma (MAC) are rare developmental eye disorders. Although over 100 causative genes have been identified, the molecular spectrum and genotype–phenotype correlations remain incompletely understood, particularly in genetically diverse populations. We set out to molecularly characterize MAC in the Israeli population. Forty-seven MAC-affected individuals from 43 unrelated families were enrolled. DNA of all probands was subjected to whole exome sequencing. The most common phenotype was microphthalmia (64% of patients). Definite or possible molecular diagnoses were achieved in 13/43 probands (30%) and involved 10 different genes (MFRP, SMO, GJA8, SOX2, RARB, TSPAN12, SHH, PTPN11, BEST1, and TP63). An in vitro splicing assay was used to explore the pathogenicity of a variant in the SMO gene. Following stringent filtering of exome data, 226 rare possibly pathogenic variants were identified in 218 genes not previously associated with MAC. The rate of molecular diagnosis achieved in this Israeli MAC cohort is similar to the reported range in other studies. The results further demonstrate the genetic heterogeneity of MAC, while supporting the involvement of complex inheritance and/or environmental factors in many of the cases. Further studies are required to reveal these underlying etiological factors, and to support the novel genotype–phenotype associations suggested here.

Biomolecules doi: 10.3390/biom16081217

Authors: Vladislava Martyshova Sergey Sedykh

Methyl-dependent restriction endonucleases are promising tools for analyzing eukaryotic DNA methylation patterns. However, quantitative assessment of their substrate specificity requires the determination of the kinetic parameters of enzymatic reactions. Here, we present a method for determining initial reaction rates based on fluorescent probes and real-time monitoring of changes in fluorescence intensity. Initial rates of methyl-dependent GlaI and BlsI restriction endonucleases were determined as the slope of the linear part of the kinetic curves, after which the Michaelis–Menten constants (KM) and reaction rates (Vmax) were calculated using nonlinear regression. For both enzymes, KM values were determined for the first time, indicating a high affinity of the methyl-dependent restriction endonucleases for methylated sites. KM values for fully methylated duplexes were in the range of (4.4–7.0)·102 nM for GlaI and 2.4–55 nM for BlsI. KM values were significantly lower for the hemimethylated duplexes: (1.9–8.0)·102 nM for GlaI and (0.7–15.0)·102 nM for BlsI; and even lower for unmethylated duplexes: (27–46)·102 nM for GlaI and (0.28–23)·102 nM for BlsI. Maximum reaction rates varied within relatively narrow limits: Vmax values were in range (4.5–19.5)·10−4 nM/s for GlaI and (1.4–18)·10−4 nM/s for BlsI, respectively. Vmax values were depended weakly on the degree of methylation compared to the KM. The proposed fluorescence method was applied to determine the kinetic parameters of methyl-dependent restriction endonucleases for the first time. It may serve as a simpler and more environmentally friendly alternative to traditional electrophoretic approaches that use radioactive labels.

Biomolecules doi: 10.3390/biom16081218

Authors: Jada Sangha David A. Hood

Skeletal muscle mitochondria possess the ability to autoregulate their health and functioning by the orchestration of mitochondrial quality control (MQC) pathways. This plasticity allows them to adapt to various stimuli, such as exercise. However, under pathological conditions, mitochondria can become dysfunctional, generating damage-associated molecular patterns (DAMPs), such as reactive oxygen species (ROS) and oxidized mitochondrial DNA (mtDNA). These DAMPs can launch an innate immune response, with consequences of widespread inflammation and atrophy. Integral to this is the NLRP3 inflammasome complex. Activation of the NLRP3 inflammasome results in maturation of caspase-1, which processes pro-inflammatory cytokines IL-1β and IL-18, as well as GSDMD. Consequently, the pore-forming GSDMD-N fragment induces pyroptosis, releasing mature IL-1β and IL-18. Exercise training is widely accepted as a potent mechanism to promote skeletal muscle health, particularly by remodeling the mitochondrial network and reducing the production of DAMPs. It has also been shown promote an anti-inflammatory milieu with the release of various myokines. Indeed, the potential of exercise to mitigate NLRP3 inflammasome-mediated inflammation and atrophy is promising. This review will examine the mechanisms underpinning inflammasome priming and activation, as well the effects of exercise, with an emphasis on the skeletal muscle.

Biomolecules doi: 10.3390/biom16081216

Authors: Büşra Başar Gökcen Büşra Atabilen Pınar Menşure Nur Çelik Zeynep Büşra Aksoy Bence Raposa Duygu Ağagündüz

Mesenchymal stem/stromal cells (MSCs) are promising candidates in regenerative medicine, but their effectiveness is significantly influenced by the surrounding metabolic and nutritional conditions. Increasing evidence suggests that lipids act not only as energy sources but also as regulators of MSC fate. This review explores how lipid metabolism influences the balance among stemness, immunomodulation, and differentiation into adipogenic or osteogenic lineages. It does so through mechanisms such as fatty acid uptake, β-oxidation, de novo lipogenesis, and membrane remodeling, all orchestrated by CD36, carnitine palmitoyltransferase 1A, PPARγ, AMP-activated protein kinase, and the PI3K/AKT/mTOR pathway. We then examine how diet reshapes the MSC lipidome: obesity and high-fat diets promote adipogenesis and senescence, while omega-3 fatty acids, caloric restriction, micronutrients, and a balanced microbiota help preserve regenerative capacity. Lastly, we discuss how combining lipidomics with multi-omics could uncover lipid-metabolic signatures and regulatory nodes that connect diet to MSC function. Overall, the diet–lipid–MSC axis emerges as a modifiable determinant of MSC function.

Biomolecules doi: 10.3390/biom16081215

Authors: Itzhak Fischer

The microtubule-associated protein tau, encoded by the MAPT gene, serves as a major component of the neuronal cytoskeleton, facilitating the assembly, stabilization, and spatial organization of microtubules. Much of the work on tau has focused on the low-molecular-weight (LMW) isoforms abundantly expressed in the central nervous system (CNS) and their pathological aggregation in tauopathies. However, a different variant known as “Big tau”, present in the peripheral nervous system (PNS) and selective CNS regions has distinct structural and functional properties and offers a unique perspective on protein evolution. Big tau is characterized by the inclusion of a large, alternatively spliced insert termed exon 4a, which expands the protein’s projection domain by approximately 250 amino acids and increases the molecular weight to 90–110 kDa. The evolutionary trajectory of exon 4a presents a fascinating enigma that challenges conventional models of protein conservation. Across the vertebrate phylogeny, spanning from fishes, amphibians and birds to mammals, the primary amino acid sequence of exon 4a exhibits extreme divergence, often reaching background levels of identity when comparing distant classes. In contrast, the physical length of this domain remains remarkably stable, hovering around the 250-amino acid mark regardless of the species. This pattern suggests that the selective pressure acting on Big tau is not directed toward specific sequence motifs or functional domains, but rather toward the biophysical properties and physical dimensions of the domain. Here, we posit that exon 4a evolved as an essential molecular spacer optimized for the structural demands of long-projection neurons and high-caliber axons as well as a protective structure for the pathologic aggregation of tau. The paper examines the genomic architecture and biophysical identity underlying the stable-size and low sequence identity of exon 4a, presenting two evolutionary mechanisms as working hypotheses: a Prototype Model of neutral drift of an ancient insert, and an Independent Exonization of convergent recruitment of non-coding DNA by transposable elements or intron retention. Finally, we emphasize the need for additional experimental work in vitro and in vivo to resolve unanswered questions about the structure of the 4a exon, the physiological role Big tau and its potential insight into tauopathies therapeutics.

Biomolecules doi: 10.3390/biom16081214

Authors: Ulan Sarsenbayeva Didier Gasparutto Nicolas Geacintov Alexander A. Ishchenko Gulzhan Zhamanbayeva Kamalidin O. Sharipov Carlos H. Trasviña-Arenas Sheila S. David Dmitry O. Zharkov Bakhyt T. Matkarimov Murat Saparbaev Sabira Taipakova

The Escherichia coli adenine-DNA glycosylase (MutY) and its human homologue, MUTYH, protect cells against oxygen-free radical-induced mutagenesis by excising regular adenine impaired with 8-oxo-7,8-dihydro-guanine (8oxoG) in the base excision repair (BER) pathway. However, removal of adenine by MutY and MUTYH from an A·8oxoG pair generated via misincorporation of an oxidized nucleotide during DNA synthesis might induce A·T→C·G transversions. Here, to examine MutY and MUTYH in vitro activities, we used short synthetic DNA duplexes in which the target adenine residue was positioned opposite a variety of DNA base modifications. MUTYH does not excise mismatched adenine in non-canonical DNA substrates, whereas MutY excises adenine mispaired with 1,3-d(GpNpG) cisplatin intra-strand crosslink. In addition, we characterized four MUTYH variants associated with cancer risk, which exhibit the following order of DNA glycosylase deficiency: WT ≥ G169D > G202E ≈ Y165C >> D222N. Human adenine-DNA glycosylase MUTYH and its mutant variants, contrary to bacterial MutY, are not prone to aberrant removal of regular adenine residues opposite modified residues in DNA duplexes. We hypothesize that E. coli MutY is prone to aberrant repair under certain conditions and that this may prevent incorporation of adenine opposite blocking lesions in the template strand.

Biomolecules doi: 10.3390/biom16081213

Authors: Bianka Nicolle Pena Marcelino Kiersten Girard Lauren Letourneau Andrew Lewin David Lewin Anna Presicci Luke Reistrom Tyler Williams H. John Sharifi

Sulforaphane (SFN), a natural compound found in cruciferous vegetables, mobilizes the transcription factor NRF2 to protect macrophages from HIV-1. SFN/NRF2 exerts this protective effect by promoting the reduced phosphorylation of the antiviral protein SAMHD1. Phosphorylation at threonine 592 (T592) potently inhibits the capacity of SAMHD1 to restrict HIV-1. How SFN, and other NRF2 mobilizers reduce SAMHD1 T592 phosphorylation is unclear. p21 (CDKN1A) is an NRF2-responsive protein that accumulates in primary macrophages after SFN treatment. p21 blocks SAMHD1 T592 phosphorylation through the inhibition of several cyclin-dependent kinases. We therefore hypothesized that SFN acts through p21 to reduce SAMHD1 T592 phosphorylation in macrophages. Here, we use RNAi, CRISPR-Cas9, and pharmacological inhibition to deplete or delete p21 in macrophages and demonstrate that p21 is necessary for SFN to efficiently reduce SAMHD1 T592 phosphorylation and restrict HIV-1 transduction.

Biomolecules doi: 10.3390/biom16081212

Authors: Isabell Schütt Jonathan Teuffel Ben H. Hlawatschke Philip Einwohlt Bernd Kreikemeyer Rebecca C. Wade Tomas Fiedler

Streptococcus cristatus (S. cristatus) belongs to the viridans group of streptococci and is a commensal of the human upper respiratory tract. With the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase, GapN, and the oxidative part of the pentose phosphate pathway (oxPPP), S. cristatus can use two different metabolic pathways to provide reduced nicotinamide adenine dinucleotide phosphate (NADPH), an essential cofactor of anabolic reactions such as fatty acid and amino acid biosynthesis. Regarding their NADP-reducing capacity, streptococci can be categorized into three groups: those that have only GapN, those that use only the oxPPP, and those that use both pathways. Here, we report on the experimental and computational characterization of the catalytic properties of the three NADP-reducing enzymes: GapN, glucose-6-phosphate dehydrogenase (G6PDH), and 6-phosphogluconate dehydrogenase (6PGDH) of S. cristatus. Kinetic analyses showed moderate substrate and cofactor affinities, with GapN displaying the tightest substrate binding, followed by 6PGDH and G6PDH, in agreement with structural and computational predictions. All three enzymes preferentially utilized NADP+, with only G6PDH exhibiting limited NAD+ promiscuity. Growth-phase-dependent activity patterns suggest dynamic adjustment of NADPH-generating pathways, with reduced GapN contribution and sustained oxPPP activity in the stationary phase. Regulatory screening indicated limited allosteric control, though feedback inhibition by NADPH and the ATP sensitivity of G6PDH point to conserved redox regulatory mechanisms. Comparative analysis across streptococci supports the concept that the coexistence of GapN and the oxidative pentose phosphate pathway in S. cristatus may provide metabolic flexibility by offering alternative routes for NADPH generation.

Biomolecules doi: 10.3390/biom16081211

Authors: Bryony Davies Faheem Seedat Lina Bergman Catherine Cluver Angga Wiratama Lokeswara Michelle Ma Morganne Wilbourne Shuhan Jiang Antonio Galvez Adam Handel Andrew Fower Carlos Escudero Wei Zhang Manu Vatish

Circulating small extracellular vesicles (sEVs) released from the placenta carry bioactive compounds. Placental sEVs (psEVs) have been implicated as drivers of pathology in preeclampsia, a common disorder of pregnancy. This study investigates the hypothesis that psEVs are detectable in cerebrospinal fluid (CSF) during pregnancy, and are present at higher concentrations in preeclamptic and eclamptic pregnancies. Two techniques were used to search for psEVs. Firstly, the ExoCounter assay was performed on neat CSF from normotensive, preeclamptic and eclamptic pregnancies, and non-pregnant controls (n = 11, 12, 10 and 4, respectively). Quantitative PCR was used to search for psEV-associated microRNAs in the CSF of pregnant women. Neither assay found evidence of psEVs in the CSF of pregnant women, regardless of whether they had preeclampsia or eclampsia. This study suggests that psEVs do not reside in CSF during pregnancy and may be more likely to impact central nervous tissues through peripheral changes or interaction with the blood–brain barrier without crossing.

Biomolecules doi: 10.3390/biom16081210

Authors: Rui Pu Guo-Pan Gong Wen-Li Song Yue Yin Zi-Yang Chen Pan Jin

Skeletal disorders, including osteoporosis, osteoarthritis, rheumatoid arthritis, and osteonecrosis of the femoral head, are common chronic conditions that substantially affect health and quality of life. Ferroptosis, a form of regulated cell death driven by iron-dependent lipid peroxidation, has increasingly been implicated in abnormal bone remodeling, cartilage degeneration, synovial pathology, and impaired skeletal homeostasis. Aerobic exercise is an important non-pharmacological approach for maintaining skeletal health, but the role of ferroptosis in its protective effects remains incompletely understood. Previous reviews have mainly discussed ferroptosis in skeletal disorders or the beneficial effects of exercise on skeletal health as separate topics. In contrast, this review places aerobic exercise, ferroptosis, and skeletal disorders within a unified framework and summarizes current evidence across osteoporosis, osteoarthritis, rheumatoid arthritis, and osteonecrosis of the femoral head. We further discuss how aerobic exercise may influence ferroptosis through the regulation of iron homeostasis, lipid peroxidation, antioxidant defense, and inflammatory responses, with attention to recently emerging molecular evidence and to the distinction between direct findings from bone- and joint-related tissues and supportive evidence from non-skeletal systems. Current direct evidence is concentrated mainly in osteoblast-related bone loss and osteoarthritis and is derived predominantly from animal and cellular studies, whereas direct clinical evidence in humans remains limited. Overall, available evidence supports ferroptosis as a potential mechanistic link between aerobic exercise and skeletal protection, but its role in mediating exercise-induced benefits in humans has yet to be established. Further clinical validation of this relationship may help clarify the biological basis of aerobic exercise interventions and support the development of more targeted exercise strategies for the prevention and management of skeletal disorders.

Biomolecules doi: 10.3390/biom16081209

Authors: Pavel Čabart

The bromodomain adjacent to zinc finger (BAZ) family protein TIP5 (transcription termination factor I (TTF-I)/interacting protein 5) contains a plant homeodomain (PHD) zinc finger module that recognizes unmodified histone H3 lysine 4. This study demonstrates that the immobilized PHD domain recruits the histone octamer complex. Depletion of zinc cations from the finger or disruption via mutagenesis completely abolished this interaction. Interestingly, the binding ability of the depleted protein was partially recovered under high concentrations of KCl. Extending the PHD domain with a PHD-bromodomain (BRD) interdomain linker led to a substantial increase in binding affinity, with the magnitude progressively dependent on the linker length. To gain insight into these preferential binding interfaces, AlphaFold 3 structure predictions were performed. Within the histone octamer complex, histone H3 was identified as a primary, but not sole, binding partner for TIP5 partial proteins. An increase in predicted total van der Waals interactions correlated with the presence of the linker and its extension; however, an anomaly stemming from the calculated stickiness of the short linker version was encountered. Increased hydrogen-bonding in models with the short linker mirrored the observed affinity. Conversely, the long linker reduced predicted hydrogen (H)-bonds below that for the PHD alone. Finally, structural analysis of the disrupted zinc finger motif revealed the fewest hydrogen bonds.

Biomolecules doi: 10.3390/biom16081208

Authors: Zhenzhen Wang Yuhan Fu Siqi Li Yan Zhang Tao Sun Nan Miao

Motor neurons form a highly specialized network composed of α-, β-, and γ-subtypes that coordinate skeletal muscle activity. Motor neuron diseases (MNDs), including amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA), are characterized by the progressive degeneration of this network, resulting in motor dysfunction. Emerging evidence underscores the significant roles of long non-coding RNAs (lncRNAs) in motor neuron development and disease. However, only a few have been experimentally confirmed as true ceRNA regulators, highlighting the need to differentiate validated mechanisms from mere associations or predictions. This review summarizes the regulatory roles of lncRNA-associated ceRNA networks in motor neuron development, evaluates the evidence for their involvement in MNDs, and explores their potential impact on disease progression. It also addresses current challenges, knowledge gaps, and future research directions for understanding ceRNA-mediated mechanisms and developing therapeutic strategies for MNDs.

Biomolecules doi: 10.3390/biom16081207

Authors: Adrián García Andrea Cavagnino Pau Navarro Olivier Gouin Cristina Guillem Anaïs Bobier Cristina Calabuig Nuria Caturla

Hair follicle homeostasis is influenced by hormonal pathways, the scalp microenvironment, and environmental stressors such as pollution, UV radiation, and oxidative stress. Elissara®, a polyphenol-enriched botanical ingredient, has shown benefits for scalp moisturization, barrier function, sebum regulation, and redness. Building on these scalp-level benefits, we investigated Elissara’s effects on follicular signaling, survival-associated biomarkers, oxidative damage, and androgen-related pathways as potential contributors to follicular health, using in silico, in vitro, and ex vivo models. Molecular docking (AutoDock Vina) of the main Elissara bioactives (oleuropein, hydroxytyrosol, verbascoside, carnosic acid, carnosol, and quercetin) identified SRD5A2 as a favorable predicted target, with individual binding energies ranging from −8.70 to −9.73 kcal/mol, approaching finasteride/dutasteride reference values. As an exploratory approach, simultaneous multi-ligand docking showed favorable global docking outputs for several targets, indicating that multiple bioactives could be structurally accommodated within complementary regions of the binding site. In human follicle dermal papilla cells, Elissara significantly increased BrdU incorporation to 245.70% of control at 0.002% and reduced SRD5A2 protein levels by 18.48% at 0.006%. In human scalp explants, Elissara at 200 µg/mL increased β-catenin, Bcl-2, and collagen IV under basal conditions and counteracted acute PM2.5/UVA-induced alterations in β-catenin, Ki67-positive cells, Bcl-2, IGF-1, collagen IV, and protein carbonylation. Together, these findings support the potential of Elissara as a promising nutricosmetic ingredient for supporting follicular resilience through multiple follicle-relevant pathways. Clinical studies assessing hair growth outcomes are needed to determine whether these preclinical findings translate into measurable benefits.

Biomolecules doi: 10.3390/biom16081206

Authors: Jaron Dalgleish Maurice Tohme Michael D. Pisano Wen-Hai Shao

Systemic lupus erythematosus (SLE) is a multifaceted autoimmune disease characterized by immune tolerance breakdown, immune cell dysfunction, and chronic inflammation. Cancer is a serious health problem and the second leading cause of mortality worldwide. Emerging evidence underscores the key role of metabolic dysregulation and the association with immunity and immune-related complications in cancer and SLE. Enhanced glycolysis and OXPHOS have been repeatedly reported in both diseases. Metabolic reprogramming is common in cancer cells and immune cells of SLE patients. In many cases, cancer cells and B cells rely on fatty acid oxidation to generate energy. Accordingly, key enzymes in those processes are also upregulated. This review summarizes current findings on major common metabolic dysregulation in cancer and SLE, highlighting the interplay of metabolic disturbances, mitochondrial dysfunction and disease pathogenesis. Furthermore, we explore the potential of targeting metabolic pathways as a therapeutic strategy to mitigate organ damage and improve outcomes in patients with SLE or cancer. We will also discuss the hurdles and prospective developments in metabolism-targeted therapy. We hope this review inspires collaborative work between cancer researchers and SLE clinicians and facilitates clinical application of cancer-metabolism-targeted drug in SLE patients.

Biomolecules doi: 10.3390/biom16081205

Authors: Loredana Bury Silvia Sorrentino Emanuela Falcinelli Giuseppe Guglielmini Antonietta Ferretti Paola Concolino Ana Sánchez-Fuentes José Rivera Paolo Gresele Erica De Candia

GPIV (CD36) is a multifunctional membrane protein expressed on various cells, including platelets, where it plays a role in adhesion and activation through the interaction with its ligands, including collagen types I and III and thrombospondin 1. Inherited GPIV deficiency, historically recognized in anti-Naka alloimmunized East Asian donors, is considered asymptomatic and associated with normal platelet aggregation, although impaired adhesion under high-flow conditions has been reported. Here, we reconsider the molecular basis, epidemiology and functional consequences of GPIV deficiency and report four unrelated patients in whom heterozygous CD36 variants are associated with markedly reduced platelet GPIV expression and a clinically relevant mucocutaneous bleeding diathesis. Patients suffered lifelong bleeding symptoms despite normal light-transmission aggregometry and platelet granule content and release and displayed decreased GPIV expression. Three of them showed slightly decreased VWF. Platelet adhesion to Type I collagen was reduced at high shear. These cases suggest for the first time an association between CD36 gene variants and bleeding and underscore the importance of including GPIV in the diagnostic workup of inherited platelet disorders, particularly when conventional assays do not reveal abnormalities.

Biomolecules doi: 10.3390/biom16081204

Authors: Ziling Tang Yuhao Liu Huanhuan Zhang Qing Zhai Liuyi Fan Xin Zhang Du Li Long Chen Xiang Li

Bursicon, a heterodimeric neuropeptide composed of Burs-α and its binding subunit Partner of bursicon (Pburs), is primarily known to regulate insect cuticle tanning and also participates in wing expansion, reproduction and immunity. Pburs is highly expressed during pheromone gland (PG) maturation in female Helicoverpa armigera, a major agricultural pest, indicating its potential role in PG development and function. In this study, we cloned the full-length coding sequence of HaPburs and verified its high conservation across insects. qPCR revealed PG transcripts peaking at 48 h post-emergence in scotophase. RNAi-mediated knockdown reduced HaPburs transcript levels by 60.01%, resulting in abnormal PG morphology characterized by irregular melanized protrusions. Silencing HaPburs lowered the major sex pheromone component (Z)-11-hexadecenal by 42.66%, reduced male attraction and mating rates to 59.15% and 56.25% of controls, and markedly decreased cumulative fecundity. HaPburs-knockdown significantly downregulated the transcription of HaPKA and HaACC, two key genes involved in sex pheromone biosynthesis. These results suggest that HaPburs mediates PG morphogenesis and sex pheromone biosynthesis, further modulating sex pheromone-mediated reproductive communication in H. armigera. The study expands the known reproductive functions of bursicon and provides a promising molecular target for eco-friendly pest management.

Biomolecules doi: 10.3390/biom16081202

Authors: Mikel Gurrea-Rubio Sophie Sloan Aditya Chada Camila I. Amarista Kohei Maeda Phillip L. Campbell Pei-Suen Tsou Laura A. Cooney Max S. Wicha David A. Fox

Triple-negative breast cancer (TNBC) is associated with recurrence, metastasis, and limited durable responses to immunotherapy, in part due to persistence of breast cancer stem cells (BCSCs). We investigated whether CD6-directed immunotherapy with the monoclonal antibody UMCD6 enhances immune-mediated killing and alters function of BCSC in stem cell-enriched TNBC models. The SUM-149 and SUM-159 cell lines were analyzed for CD6 ligand expression, cocultured with human peripheral blood mononuclear cells (PBMCs) treated with UMCD6, pembrolizumab, or isotype control, and assessed by live-cell cytotoxicity imaging, flow cytometry, soft agar colony formation, and extreme limiting dilution sphere assays. Both TNBC lines co-expressed the CD6 ligands CD44, CD166/ALCAM, and CD318/CDCP1. UMCD6 significantly increased PBMC-mediated apoptosis and reduced tumor cell survival in both models, with greater activity than pembrolizumab under these in vitro conditions. In surviving SUM-159 cells, UMCD6 reduced the ALDH+ population wit×hout significantly altering CD44+CD24− frequency, indicating preferential effects on a distinct stem-like compartment. Functionally, UMCD6 decreased anchorage-independent colony formation and reduced sphere-forming frequency from 1/33.6 to 1/68.3 cells (p = 0.0186). These findings identify the CD6 ligand axis as a therapeutic vulnerability in BCSC-enriched TNBC and support further preclinical evaluation of CD6-directed immunotherapy as a strategy to enhance antitumor immunity while limiting tumor-initiating capacity.

Biomolecules doi: 10.3390/biom16081203

Authors: Zhanna Rakhimbayeva Abdujalil Mussayev Ainash Oshibayeva Gulnaz Nuskabayeva Saltanat Kyrykbayeva Lazzat Begimbekova Saltanat Khudaibergenova Karlygash Sadykova Zhanar Zhagiparova Mohamad Aljofan

Background: Mare’s milk has gained attention as a functional food due to its bioactive compounds and potential microbiome-modulating properties. This systematic review evaluated the evidence on its potential role in gut microbiome restoration and immune modulation following COVID-19, particularly in pediatric and maternal populations. Methods: PubMed/MEDLINE, Scopus, Web of Science, and Embase were systematically searched for studies investigating mare’s milk or koumiss and their effects on gut microbiota, immune responses, inflammatory markers, or gastrointestinal outcomes. Results: Eight studies were included: five examined COVID-19-associated gut microbiome alterations, and three investigated the biological effects of mare’s milk or fermented mare’s milk. COVID-19 was consistently associated with reduced microbial diversity, depletion of beneficial bacteria, and enrichment of opportunistic pathogens, with some changes persisting after recovery. Conclusions: Koumiss demonstrates biologically plausible microbiome-modulating and immunoregulatory properties that may support recovery from COVID-19-associated gut dysbiosis. However, current evidence remains indirect, and clinical studies are needed before recommendations can be made.

Biomolecules doi: 10.3390/biom16081201

Authors: Xuanbo Chen Enhui Jiang Yuta Yang Haotian Zhang Zhaoyu Liu Ebadu Areb Yongsheng Wang Xianyong Lan

Clock genes, such as cryptochrome 1 (CRY1), exhibit rhythmic expression in the reproductive organs. This gene is a key component of the circadian clock and is involved in various physiological processes, including reproduction, suggesting that it may be linked to ovarian activity via neuroendocrine pathways. However, the association between CRY1 variants and ovarian traits in dairy cows is unclear. In this study we used qRT-PCR to assay the mRNA expression of this gene, and found that CRY1 expression was highest in oocytes in several tissues; subsequently, we found that CRY1 expression was highest in the ovary in Chinese Holstein dairy cattle, followed by muscle and spleen tissues (p < 0.01). Next, we identified a six bp insertion/deletion (indel) locus within the CRY1 gene in Chinese Holstein dairy cattle. Only two genotypes were detected: II (n = 854, 83.7%) and ID (n = 166, 16.3%). Association analysis revealed that the identified indel was significantly associated with dominant follicle and corpus albicans diameters (p < 0.05) during metestrus. Specifically, individuals with the ID genotype exhibited smaller dominant follicles and corpus albicans than those with the II genotype. Our preliminary findings suggest that CRY1 is associated with specific ovarian morphological traits and may serve as a basis for further investigation of its potential role in bovine reproductive function.

Biomolecules doi: 10.3390/biom16081200

Authors: Sukanya Horpaopan Esther Schamschula Heidelinde Fiegl Hannes Dapoz Christina Lutz-Nicoladoni Simon Schnaiter Albert Amberger Ulrich Strasser Renate Lunzer Andreas von der Heidt Katalin Csanaky Johannes Zschocke Katharina Wimmer

The identification of a pathogenic variant (PV) in one of the mismatch repair (MMR) genes confirms the diagnosis of Lynch syndrome (LS). Hence, the correct classification of MMR gene variants is of utmost importance for appropriate counselling, surveillance, and treatment of LS patients and their families. In 7/200 unrelated Tyrolean-suspected LS patients, we identified the rare variant MLH1:c.836T>G. Clinical and tumor data strongly indicate that this founder variant is associated with an increased risk for early-onset LS-associated tumors. We also demonstrate that the variant leads to aberrant mRNA splicing. However, the splice effect’s leakiness together with the small effect of the amino acid change p.(Val297Gly) encoded by the residual full-length transcripts in a functional assay preclude its formal classification as (likely) PV according to internationally accepted variant interpretation guidelines. The family histories of the carriers suggest that the obstacles to classify the variant as (likely) PV may be related with a reduced penetrance. Nonetheless, and despite the formal classification of MLH1:c.836T>G as a variant of uncertain significance, we show that carriers should undergo cancer surveillance and predictive testing should be offered to relatives. This variant illustrates the need for an improved classification framework for appropriate categorization of lower-penetrance alleles.

Biomolecules doi: 10.3390/biom16081199

Authors: Sheila Ngumbi Mohamed S. Gad Kara Ye Sarah Ye Christie Taylor Mostafa Mahrous Manuela Bartoli

In recent years, the role of non-coding RNAs in human physiology and pathology has emerged as an essential avenue of investigation. Among others, studies identifying the biological role of microRNAs (miRNAs) have paved the way for future inquiries on the importance and biological significance of non-coding RNAs. In this review, we provide an overview of miRNAs’ biology and their contribution to the pathogenesis of diabetic retinopathy (DR). This complication of diabetes is the leading cause of blindness in adults, affecting more than 4 million people in the US alone and over 103 million people worldwide. Despite the tremendous efforts of the scientific community and the pharmaceutical industry, the development of new, more effective therapeutic and diagnostic tools for DR to date remains an unmet need. More than a decade from the initial work assessing miRNA expression profiles in diabetic patients, we have learned the impact of these signaling molecules in DR and garnered knowledge of their complexity and their potential as new diagnostic and therapeutic targets for this potentially blinding condition.

Biomolecules doi: 10.3390/biom16081198

Authors: Rongjie Fu Yalong Wang Ishita Rehman Ella Bedford Sana Sharif Nghi D. Nguyen Reid T. Powell Andrew Adams Weijun Liu Shuyue Wang Wei He Yue Lu Bin Liu Pooja Anil Shah Jordi Rodon Ahnert Taiping Chen Weiyi Peng Clifford C. Stephan Xinli Liu Mark T. Bedford Han Xu

Protein arginine methyltransferase 5 (PRMT5) is a synthetic lethal target in methylthioadenosine phosphorylase-deleted (MTAP-null) cancers. Second-generation methylthioadenosine (MTA)-cooperative PRMT5 inhibitors preferentially target MTAP-null cells while largely sparing MTAP-wildtype (MTAP-WT) cells, thereby improving tumor selectivity over first-generation PRMT5 inhibitors. Despite encouraging efficacy and safety signals in early clinical studies, the modest objective response rates (ORRs) observed with these inhibitors suggest that intrinsic or acquired resistance may limit their clinical benefit. Here, we investigated acquired resistance to the MTA-cooperative PRMT5 inhibitor BMS-986504/MRTX1719 in MTAP-null non-small cell lung cancer (NSCLC) cells and sought to identify therapeutic vulnerabilities that emerge upon resistance. Using multiple in vitro-derived resistant models, we found that acquired resistance was accompanied by cross-resistance to mechanistically distinct PRMT5 inhibitors. Notably, this phenotype was not fully explained by altered PRMT5 activity or changes in MTA levels. High-throughput drug screening of paired sensitive and resistant cells revealed increased sensitivity to MEK inhibitors following acquisition of MRTX1719 resistance in KRAS-wildtype NSCLC cells. Consistently, resistant cells exhibited rewired MAPK-related transcriptional programs. Together, these findings identify MEK inhibition as a reproducible collateral vulnerability associated with acquired MRTX1719 resistance in MTAP-null NSCLC models and support further evaluation of MEK inhibition as a potential treatment-switching strategy following resistance.

Biomolecules doi: 10.3390/biom16081197

Authors: Kyu-Ho Yi

Background: Mitochondrial dysfunction is increasingly recognized as a central contributor to intrinsic skin aging, photoaging, cellular senescence, impaired extracellular-matrix homeostasis, dysregulated pigmentation, and delayed recovery after energy-based or minimally invasive procedures. Pyrroloquinoline quinone (PQQ) is a redox-active ortho-quinone that has attracted interest because it can participate in repeated redox cycling, protect mitochondrial function, and activate signaling associated with mitochondrial biogenesis. Objective: This narrative review evaluates the mechanistic basis, available dermatologic evidence, translational opportunities, and major uncertainties surrounding PQQ as a mitochondrial rejuvenation strategy in aesthetic dermatology. Methods: PubMed/MEDLINE and Europe PMC were searched from database inception through 10 August 2026 using PQQ-, mitochondrial-, skin-, delivery-, and safety-related terms; reference lists were also screened. Mechanistic, preclinical, skin-focused, human, and regulatory evidence was synthesized narratively. Results: Experimental studies support PQQ-mediated activation of mitochondrial biogenesis pathways and protection against oxidative injury in several cell and animal systems. Skin-specific evidence includes attenuation of oxidative stress, DNA damage, senescence markers, and matrix metalloproteinases in accelerated-aging mouse models; protection of UVA-exposed human dermal fibroblasts; suppression of UVB-induced caspase-1 release in keratinocytes; a small oral dry-skin study; and a multi-ingredient topical study containing an allyl PQQ derivative. These studies do not establish PQQ-specific clinical aesthetic efficacy. Conclusion: PQQ is a biologically plausible mitochondrial-support compound, but it should currently be regarded as an investigational ingredient rather than an established aesthetic treatment. Carefully designed formulation, toxicology, dose-finding, biomarker, and randomized clinical studies are required before claims regarding wrinkle reduction, pigment improvement, enhanced collagen production, or accelerated post-procedure recovery can be justified.

Biomolecules doi: 10.3390/biom16081196

Authors: Kuo-Tzu Sung Dau-Ming Niu Shu-Fen Hsu Ming-En Liu Po-Lin Lin Yau-Huei Lai Hsiang-Wei Yang Yung-Hsiu Lu Cheng-Ting Tsai Ta-Chuan Hung Po-Sheng Chen Chung-Lieh Hung

Right ventricular global longitudinal strain (RVGLS) and right ventricular free-wall longitudinal strain (RVFWLS) are both used to assess right ventricular involvement, but they include different myocardial components. We examined their cross-sectional correlates and longitudinal changes associated with enzyme replacement therapy (ERT) in 100 patients with genetically confirmed Fabry disease, including 69 with serial echocardiography. RVGLS was independently associated with left ventricular global longitudinal strain (LVGLS; standardized β = 0.466, p < 0.001) and interventricular septal thickness (standardized β = 0.257, p = 0.027), whereas RVFWLS was independently associated with right atrial reservoir strain (standardized β = −0.542, p < 0.001). RVGLS and RVFWLS were not significantly correlated (r = 0.053, p = 0.654). In the paired RV strain subgroup, longitudinal RVGLS change differed between untreated and ERT-treated patients (+2.06 ± 3.94% vs. −1.28 ± 3.64%, p = 0.017), whereas RVFWLS change did not (p = 0.838). In a sensitivity model adjusted for age, sex, genotype, and baseline RVGLS, ERT remained associated with ΔRVGLS (β = −3.28 percentage points, 95% CI −5.25 to −1.32; p = 0.001). These findings identify different correlates of septal-inclusive and free-wall RV strain and require prospective validation.

Biomolecules doi: 10.3390/biom16081195

Authors: Jiuyi Li Niya Tu Laura C. Miller Yongming Sang

The porcine interferon (IFN) system is highly diversified, particularly within Type I subfamilies, yet its evolutionary trajectory across domestication and breed formation remains poorly characterized. We performed a comprehensive comparative genomic and structural analysis of 432 IFN sequences spanning all IFN types across 11 Sus scrofa breeds representing commercial, indigenous, and wild/outgroup lineages. Phylogenetic reconstruction, pairwise dN/dS selection pressure analysis, and AlphaFold2-based 3D structure prediction coupled with DALI structural similarity mapping were integrated to resolve repertoire architecture, evolutionary constraints, and domestication-associated divergence. IFN repertoire organization is governed primarily by family identity rather than breed origin, with Type I IFN-α, -δ, and -ω subfamilies showing pronounced gene expansion in domestic breeds. Phylogenetic clustering and structural similarity consistently grouped sequences by subtype, independent of domestication history. Pervasive purifying selection (median ω = 0.48) maintained functional constraints across all lineages. Commercial breeds exhibited significantly higher within-category structural convergence alongside expanded repertoires, while structural conservation was evolutionarily decoupled from sequence-level selective pressure. Domestication potentially drove coordinated IFN repertoire expansion and structural conservation with related purifying selection at the gene level. These findings establish a genomic framework linking breed-specific IFN architecture to antiviral capacity and provide a foundation for immunogenetic-informed breeding strategies in the swine model.

Biomolecules doi: 10.3390/biom16081194

Authors: Guanglin Zhang Pavan Thapak

Traumatic brain injury (TBI) and non-acquired brain damage represent a catastrophic global health burden, frequently resulting in persistent neurological impairment, long-term cognitive decline, and increased susceptibility to secondary psychiatric disorders [...]

Biomolecules doi: 10.3390/biom16081193

Authors: Zhenzhong Tang Shuangyuan Fan Guanhong Lin Tangtao Yuan Shuang Yang

Calcium ions (Ca2+) function as ubiquitous second messengers that translate environmental and developmental cues into spatially and temporally defined cellular responses in plants. This review summarizes the cellular architecture and molecular mechanisms that generate, shape, and terminate Ca2+ signals, with emphasis on plasma-membrane channels, intracellular stores, pumps, exchangers, and organelle-associated transport systems. We also examine the development of live Ca2+ indicators, from chemical dyes and aequorin to ratiometric and single-fluorophore genetically encoded calcium indicators, and discuss principles for selecting sensors for different tissues and subcellular compartments. Recent studies have applied these tools to abiotic stress, plant immunity, polar growth, development, symbiosis, and systemic signaling. Accurate quantitative imaging nevertheless requires careful matching of sensor properties to the target cellular environment and rigorous control of motion, spectral interference, and analytical procedures. Combining improved indicators with advanced microscopy, genetic validation, and standardized data analysis should help connect distinct Ca2+ signatures with their molecular origins and physiological roles.

Biomolecules doi: 10.3390/biom16081192

Authors: Chayeen Brotzki da Costa Péter Németh Péter Engelmann

The impact of epigenetic mechanisms on molecular and cellular processes of regeneration remains a less-investigated field, especially concerning earthworm segment restoration. To evaluate distinct methylated cytosines under different conditions, earthworm segments were collected: decitabine-treated and controls; anterior and posterior amputation; intact and regenerated (2- and 4-week). 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) distribution in tissues was assessed by immunohistochemistry (IHC), and in genomic DNA by dot blot. DNA-methyltransferase (DNMT) and ten-eleven translocation (TET) dioxygenase activity was determined by immuno-based colorimetry. DNMT1 and TET gene expressions were verified with real-time PCR. Decitabine treatment reduced 5mC levels in most tissues, persisting in the anterior coelomic cavity (intact and blastemas). 5hmC remained elevated in most tissues, remarkably in 2-week blastemas. In the same period, DNMT and TET presented the highest activity in anterior treated samples compared to other treated periods. Concurrently, DNMT1 gene expression increased prominently in anterior segments, while TET showed the highest expression in both anterior and posterior 2-week treated groups. Thus far, our observations indicate that, despite decitabine’s effect on the DNA methylation machinery of the earthworm model, the region of amputation and the regeneration period also interfere with activity and expression of epigenetic enzymes, affecting 5mC and 5hmC distribution.

Biomolecules doi: 10.3390/biom16081191

Authors: Alim Turgaliyev Roman Konovalov Anton Borissenko Dieter Riethmacher

The extracellular matrix (ECM) in cancer differs from healthy tissue in structure, composition, and mechanical properties. Matricellular proteins (MCPs) play important roles in shaping ECM architecture during tissue remodeling. This narrative review, combined with a bioinformatics analysis, examines six major MCP families—Fasciclins, Tenascins, Thrombospondins, Small Leucine-Rich Proteoglycans, the SPARC family, and the CCN family—through a mechanobiological lens in bladder cancer. It summarizes current knowledge on the mechanical regulation of MCP expression, their effects on matrix stiffness, and their contributions to bladder cancer progression. Analyses of public datasets reveal that stromal cells are the predominant source of MCPs in the tumor microenvironment. Furthermore, mechanical upregulation and involvement in the formation of stiff ECM highlight MCPs as important players in a mechanotransduction feedback loop. While most MCPs exert pro-tumorigenic effects on bladder cancer cells, several display context-dependent or anti-tumorigenic activities. Existing studies have primarily focused on the isolated effects of MCPs on bladder cancer cell lines in two-dimensional systems or simple subcutaneous xenograft models. Both approaches fail to capture the context-dependent nature of MCPs and their involvement in ECM formation. These findings underscore the need for future studies to investigate the complex effects of MCPs on bladder cancer progression.

Biomolecules doi: 10.3390/biom16081190

Authors: Andrea Exnerová Sabina Seidlová Věra Daňková Vojtěch Pavlík Kristina Nešporová

Therapies based on mesenchymal stromal cells (MSCs) have high potential in the field of regenerative medicine due mainly to their immunomodulatory properties. However, their clinical translation is hampered by a lack of sufficiently standardised potency tests. Since macrophages constitute key mediators of the effects of MSCs, macrophage-based assays potentially provide a relevant in vitro tool for the evaluation of the activity of MSC products. This study involved the coculturing of canine adipose-derived mesenchymal stromal cells (ASCs) with macrophages derived from human THP-1 and U937 monocyte cell lines, murine RAW264.7 macrophages and primary human macrophages. The M2 polarisation was assessed following stimulation with IL-4/IL-13 in THP-1 and U937 macrophages. The mRNA expression of the pro- and anti-inflammatory markers was analysed using qPCR. The ASC transwell coculture altered the LPS-induced inflammatory mRNA expression in a strongly model- and marker-dependent manner. The U937-derived macrophages exhibited the most consistent suppression of the tested inflammatory transcripts and the RAW264.7 cells provided a practical readout for selected inflammatory markers, whereas the THP-1 macrophages evinced the suppression of TNFA but not IL1B or PTGS2 under the selected stimulation conditions. IL-4/IL-13 induced moderate but statistically non-significant changes in IL10 and TGFB1 in the U937-derived macrophages but no reproducible response in the THP-1-derived macrophages. In a subsequent U937 coculture experiment, ASC-derived paracrine factors altered selected M2-associated transcripts at specific time points. The results thus provided support for macrophage-based transcriptional readouts as an early-stage tool for comparing responder macrophage models and detecting the selected anti-inflammatory paracrine effects of canine ASCs; the U937 cells were found to be particularly suitable for the study of inflammatory polarisation and the RAW264.7 cells for the purpose of standardised screening.

Biomolecules doi: 10.3390/biom16081189

Authors: Leonard Azamfirei Vlad Dimitrie Cehan Alina Roxana Cehan Mihai Claudiu Pui Alexandra Lazar

Background: Although advances in critical care have improved short-term outcomes, sepsis survivors continue to face substantial chronic morbidity and impaired long-term survival. Conventional threshold-based tools such as the Sequential Organ Failure Assessment (SOFA) and Modified Early Warning Score (MEWS) show moderate and variable discrimination across cohorts. Reported areas under the receiver operating characteristic curve (AUROCs) must therefore be interpreted in relation to the population, prediction horizon, and outcome used in each study rather than as direct head-to-head comparisons. Objectives: This review evaluates how artificial intelligence (AI) could be linked with dynamic plasma metabolites, particularly citrulline and β-hydroxybutyrate (3-HB), to support biologically informed sepsis phenotyping, while critically examining mechanistic evidence, clinical limitations, and translational readiness. Data Synthesis: Machine-learning and natural language processing architectures have shown promising discrimination in many early-detection studies, with pooled AUROCs near 0.87 and reported prediction windows extending to 48 h. However, performance estimates vary with cohort composition, outcome definition, and validation design, and they should not be ranked against unrelated biomarker studies. Human sepsis studies generally associate low or persistently low citrulline with impaired intestinal function and organ injury, but no sepsis-specific decision cutoff has been externally validated. For 3-HB, an AUROC of 0.8429 for septic liver injury was derived from a cohort of 57 patients and has not been shown to add value beyond routine liver tests or illness-severity measures. Murine experiments provide mechanistic hypotheses for ketone-mediated organ protection, but model-specific and sometimes opposing nutritional effects limit direct translation. These metabolites are therefore best considered candidate longitudinal features for multimodal phenotyping rather than stand-alone clinical triggers. Conclusions: Biologically informed algorithmic surveillance is a promising direction, but clinical implementation requires prospective serial sampling, explicit adjustment for renal, hepatic and nutritional confounders, head-to-head comparison with routine markers, and external validation of calibration and clinical utility. Until these requirements are met, citrulline and 3-HB should support research phenotyping rather than direct treatment selection.

Biomolecules doi: 10.3390/biom16081188

Authors: Andrew G. Smith

In the biosynthesis of heme the tetrapyrrole hydroxymethylbilane is converted enzymatically to uroporphyrinogen III whereas conversion to uroporphyrinogen I occurs spontaneously. Both are substrates for uroporphyrinogen decarboxylase (UROD) but only the III isomer is a precursor of heme. These porphyrinogens are easily oxidised to the respective uroporphyrins and trace amounts occur in the urine of healthy humans and animals. Large quantities of uroporphyrins I and III, as well as other oxidation products, occur in the liver and urine of patients with some porphyrias and after poisoning of people and animals by chemicals, such as hexachlorobenzene (HCB) and 2,3,7,8-tetrachorodibenzo-p-dioxin (TCDD). In the acquired disorder sporadic porphyria cutanea tarda (sPCT) and chemical-induced porphyria, hepatic UROD is inhibited, ostensibly by a partially oxidised uroporphyrinogen. The processes leading to oxidation of the uroporphyrinogens are interactions of a variety of external, internal and genetic factors. In some experimental systems, cytochrome P450 1A2 is implicated in the oxidation of uroporphyrinogens and uroporphyria and many patients and in vivo studies demonstrate the influence of iron. The article reviews the present state of knowledge of uroporphyrinogen oxidation, susceptibility and outcomes, and illustrates areas that require further exploration to explain fully the mechanisms of sPCT and the related uroporphyria caused by chemicals of toxic concern.

Biomolecules doi: 10.3390/biom16081187

Authors: Song Bai Chenfan Geng Wei Wang Xiaoyu Yan Tian Dong Hailiang Song Hongxia Hu

Masu salmon (Oncorhynchus masou) is an ecologically and economically important cold-water salmonid in East Asia that exhibits diverse life-history forms. To compare population-level genomic variation and patterns of homozygosity among fish from different sources, we analyzed whole-genome resequencing data from 465 individuals representing one field-collected Tumen River population (TM) and two landlocked cultured populations from Chicheng (CC) and Yanji (YJ). After quality control, 6,220,980 high-quality SNPs were retained. Population-specific filtering identified 5,589,828, 3,545,209, and 4,975,751 polymorphic SNPs in CC, TM, and YJ, respectively; although SNP numbers differed, approximately 91% of variants in each population were located in intronic or intergenic regions. Principal component analysis, ADMIXTURE, and distance-based neighbor-joining analysis clearly distinguished the three populations, with CC and YJ showing the closest genetic relationship. Pairwise FST was lowest between CC and YJ and highest between TM and YJ. CC exhibited the highest linkage disequilibrium, whereas TM showed the fastest LD decay and the lowest nucleotide diversity and heterozygosity. Runs of homozygosity (ROH) burden was highest in TM, intermediate in CC, and lowest in YJ. TM had the highest number of ROHs, cumulative ROH length, and FROH, and ROHs longer than 5 Mb were detected only in this population. CC had an intermediate ROH burden dominated by short segments, whereas YJ had the lowest ROH-based genomic inbreeding. The high and heterogeneous ROH burden in TM indicates elevated genome-wide homozygosity among the sampled fish but does not, by itself, demonstrate recent inbreeding throughout the population. Candidate ROH islands and their annotated genes showed limited overlap among populations. Candidate genes in TM were primarily associated with ion regulation, neural processes, and energy metabolism, whereas those in CC and YJ shared broad functional categories involving development, muscle organization, nutrient transport, and neural regulation but differed in most specific genes. These regions and genes should be regarded as exploratory, hypothesis-generating candidates rather than evidence of selection or causality. Overall, this study reveals distinct population genomic characteristics and ROH patterns among masu salmon populations of different origins and provides a basis for future germplasm conservation and genetic management.

Biomolecules doi: 10.3390/biom16081186

Authors: Yuying He Jun Gao Qiang Li Chuxi Zhang Mingrui Zhai Yuehua Liu

Obstructive sleep apnea (OSA) is characterized by chronic intermittent hypoxia (CIH), which contributes to systemic metabolic disorders. However, the mechanisms underlying CIH-induced intestinal dysfunction remain unclear. In this study, we investigated the effects of CIH on intestinal barrier integrity, gut microbiota, and host metabolism using a multi-omics approach. Male C57BL/6J mice were exposed to six weeks of CIH or normoxia. Colonic barrier integrity was assessed by histological and molecular analyses. Gut microbiota was profiled by full-length 16S rRNA gene sequencing. Untargeted metabolomics was performed on fecal and serum samples, followed by integrated microbiome–metabolome analysis. CIH markedly impaired colonic barrier integrity, as evidenced by disrupted crypt architecture, reduced goblet cell abundance, and decreased expression of ZO-1, Occludin, and Claudin-5. CIH also induced gut microbial dysbiosis, characterized by depletion of the beneficial mucin-associated bacterium Akkermansia muciniphila and enrichment of several anaerobic taxa. Metabolomic analysis revealed opposite alterations of PC (20:2/0:0) and LysoPE (20:5/0:0) between feces and serum, whereas melatonin was consistently decreased in both compartments. Integrated multi-omics analysis further revealed close associations between microbial dysbiosis and metabolic remodeling. Collectively, these findings demonstrate that CIH disrupts intestinal homeostasis through coordinated alterations in barrier integrity, gut microbiota composition, and host metabolism, providing new insights into the intestinal mechanisms underlying OSA-associated systemic dysfunction.

Biomolecules doi: 10.3390/biom16081185

Authors: Enrico Rosa Maria Vaccaro Bruno Fionda Valentina Lancellotta Gabriele Ciasca Pierpaolo Dragonetti Lucia Di Maio Fabio Marazzi Francesco Marampon Monica Mangoni Maria Antonietta Gambacorta Marco De Spirito Luca Tagliaferri

Background: The abscopal effect refers to the clinical response of non-irradiated tumor lesions following localized radiotherapy (RT). Once regarded as a rare phenomenon, it has gained renewed interest in the era of immunotherapy, as RT may promote systemic anti-tumor immune responses. This narrative review summarizes current biological, radiobiological, and clinical evidence on the abscopal effect and highlights translational gaps limiting its reproducibility. Methods: Preclinical, translational, and clinical evidence was qualitatively analyzed across seven domains: RT, immunology, and clinical oncology. A structured qualitative gap analysis was used to identify disconnections between biological mechanisms, RT parameters, biomarkers, and clinical outcomes. Results: Current evidence supports the biological plausibility of the abscopal effect through immunogenic cell death, antigen and damage-associated molecular patterns (DAMP) release, activation of the cyclic GMP–AMP synthase–stimulator of interferon genes (cGAS-STING) pathway, dendritic-cell priming, and T-cell-mediated responses. However, clinical results remain heterogeneous. Dose, fractionation, irradiated volume, timing, lymphocyte preservation, and interventional RT (modern brachytherapy, IRT) may influence systemic immune activation. Emerging biomarkers, particularly extracellular vesicles (EVs), may help connect radiation-induced biological stress with immune modulation and clinical response. Conclusions: The main barrier to clinical translation is the fragmentation of evidence across RT, immunology, and clinical oncology. Integrated translational frameworks combining dosimetry, immune monitoring, EVs-based biomarkers, imaging, and clinical endpoints may improve the interpretation and reproducibility of abscopal responses in immuno-RT.

Biomolecules doi: 10.3390/biom16081184

Authors: Sheng Liu Shuran Xing Feifei Wang He Zhu Xiaoyun Fu Yang Yu Litao Wang

Food spoilage is mainly driven by lipid oxidation and microbial proliferation. To counteract these challenges, multifunctional protective films have emerged as effective solutions for suppressing both reactions. In this work, biodegradable polylactic acid (PLA) was selected as the polymer matrix to fabricate composite films. Colloidal ZIF-8 nanoparticles loaded with the natural antioxidant astaxanthin (AST) were mixed with PLA. By precisely controlling temperature and humidity during the solution-casting process, a honeycomb-structured PLA/AST@ZIF-8 composite film was successfully prepared. The structural and physico-chemical properties of the as-prepared film were systematically characterized by FE-SEM, FTIR, Raman, XRD, and TGA. The results confirm the formation of a well-defined honeycomb morphology, with AST uniformly dispersed throughout the PLA matrix. Importantly, films with AST content above 2.0% exhibit weak antibacterial properties. Practical application tests for preserving beef tenderloin demonstrate that the film provides excellent antioxidant and antibacterial effects. On the seventh day, the water loss, pH, ΔE and total volatile basic nitrogen (TVB-N) values of beef samples treated with the PLA/ZIF-8/2.5%AST film remained within acceptable thresholds, effectively extending the shelf life of fresh meat. Safety assessments on overall migration (OM) and Zn2+-specific migration confirm that the PLA/AST@ZIF-8 composite film fully complies with EU Regulation No. 10/2011. These results demonstrate the great application prospects of the composite film for high-performance food preservation.

Biomolecules doi: 10.3390/biom16081183

Authors: Predrag Jancic Ivana Kovac Halil Emre Demirtas Nebojsa Nick Knezevic Graham Trevor Lubinsky

Postoperative cardiovascular complications remain a leading cause of morbidity and mortality after noncardiac surgery, yet current risk models do not incorporate psychosocial stress. With over 300 million noncardiac surgeries performed annually worldwide and a substantial burden of perioperative cardiovascular complications, preoperative chronic stress is increasingly recognized as a potentially modifiable risk factor. Chronic stress produces HPA axis dysregulation, glucocorticoid resistance, sympathetic activation, inflammation, endothelial dysfunction, and hypercoagulability. These pathways overlap with the mechanisms underlying perioperative myocardial injury, arrhythmogenesis, and venous thromboembolism. Prospective data demonstrated that preoperative psychological distress independently predicted 30-day cardiovascular complications and 1-year mortality after noncardiac surgery. Allostatic load studies in noncardiac surgery patients showed that high preoperative physiological burden was associated with up to twofold increases in postoperative mortality and elevated rates of myocardial infarction and venous thromboembolism. Epidemiological evidence further supports that anxiety and depression independently increase cardiovascular risk. Converging evidence suggests that preoperative psychological distress is a relevant perioperative cardiovascular risk factor. However, no randomized controlled trial has evaluated whether targeted preoperative stress reduction can decrease postoperative cardiovascular events, representing a critical gap warranting prospective investigation.

Biomolecules doi: 10.3390/biom16081182

Authors: Muin Tuffaha Wael Hananeh Ehab Shiban Michael Starke

Integrins are heterodimeric transmembrane receptors that mediate bidirectional signaling and regulate cell–cell and cell–extracellular matrix interactions. Integrin αvβ6 is an epithelial-associated integrin that has emerged as a promising molecular target for PET/CT imaging using integrin αvβ6-directed radiotracers such as 68Ga-Trivehexin, and, most recently, for antibody–drug conjugate therapy in epithelial malignancies. Unexpected physiological and incidental uptake within the pituitary gland has been reported in integrin αvβ6-targeted PET studies, including uptake in morphologically normal pituitary glands and pituitary neuroendocrine tumors (PitNETs). However, the histological basis of integrin αvβ6 expression in the human pituitary gland remains poorly understood. The aim of this study is to characterize the immunohistochemical expression of integrin αvβ6 in normal human pituitary tissue and PitNETs and to evaluate its potential implications for integrin αvβ6-targeted imaging and theranostic applications. Five complete adult pituitary glands obtained at autopsy and 28 PitNETs were examined by immunohistochemistry for integrin αvβ6. Staining distribution, intensity, and cellular localization were assessed in the adenohypophysis, neurohypophysis, and Rathke’s cleft remnants. PitNETs were classified according to transcription factor expression (PIT1, TPIT, and SF1). Among the 28 PitNETs, 17 were SF1-lineage (60.7%), three were PIT1-lineage (10.7), two were TPIT-lineage (7.1%), three lacked a dominant transcription factor (10.7%), and three showed plurilineage expression (10.7%). Integrin αvβ6 expression was evaluated semiquantitatively according to staining intensity and the percentage of positive tumor cells. In normal pituitary glands, integrin αvβ6 immunoreactivity was predominantly membranous and localized to larger adenohypophyseal cells irrespective of transcription factor lineage or hormone phenotype. Strong expression was also observed in the epithelial lining cells of Rathke’s cleft remnants, whereas the neurohypophysis lacked detectable integrin αvβ6 expression. Among the 28 PitNETs, integrin αvβ6 expression was detected in 20 cases (71.4%). Positive tumors demonstrated variable staining intensity and extent, ranging from 20% to 100% positive tumor cells. By lineage, integrin αvβ6 expression was detected in 13 of 17 SF1-lineage tumors (76.5%), one of three PIT1-lineage tumors (33.3%), and zero of two TPIT-lineage tumors (0%). Additionally, all three tumors lacking a dominant transcription factor (100%) and all three plurilineage tumors (100%) demonstrated integrin αvβ6 expression. Eleven integrin αvβ6-positive tumors showed expression in ≥50% of tumor cells, and six exhibited strong or diffuse immunoreactivity. Integrin αvβ6 expression in adenohypophyseal cells and Rathke’s cleft remnants provides a histological explanation for physiological pituitary uptake observed on αvβ6-targeted PET/CT imaging. The high prevalence of integrin αvβ6 expression in PitNETs, particularly in a subset demonstrating strong and diffuse immunoreactivity, suggests potential applicability of integrin αvβ6-targeted molecular imaging and theranostic approaches, including both radioligand- and antibody-based strategies. However, these applications remain investigational and require further validation in preclinical and clinical studies. At the same time, physiological integrin αvβ6 expression in normal anterior pituitary tissue may limit imaging specificity and should be considered when developing integrin αvβ6-targeted radioligand therapies. Further clinicopathological and imaging correlation studies are warranted to define the diagnostic and therapeutic role of integrin αvβ6-targeted approaches in PitNETs.

Biomolecules doi: 10.3390/biom16081181

Authors: Nicholas R. Rugelis Ashok Kumar Jeffrey J. Hayes

Chromatin structure is dynamic and regulated by many factors, including enzymes that chemically modify histones and DNA, chromatin remodeling complexes that physically manipulate nucleosomes and chromatin, and non-enzymatic proteins that bind to DNA or nucleosomes to create specialized regions in chromatin. This multifactorial regulation stems from the need for fine-tuned control, which is key in processes including DNA repair, replication, and gene expression. Linker histones are a family of proteins structurally distinct from the core histones that provide a poorly understood layer of regulation in chromatin. In this review, we introduce the basics of chromatin structure, what is known about how linker histones (H1s) bind to nucleosomes and influence chromatin, and how the individual domains within H1s contribute to these activities. We especially focus on recent studies describing canonical and alternative H1-nucleosome binding and their potential roles in chromatin.

Biomolecules doi: 10.3390/biom16081180

Authors: Yanli Bai Wen Yang Zirong Wang Qianqian Yang Zhongping Zhang Jialong Liu Yafang Qi Dongling Liu

Doxorubicin (DOX) is a widely used anthracycline chemotherapeutic agent; however, its clinical application is limited by dose-dependent cardiotoxicity, which can result in progressive cardiac dysfunction and heart failure. Increasing evidence indicates that DOX-induced cardiotoxicity is closely associated with premature cardiac senescence, a pathological process distinct from physiological cardiac aging. DOX induces senescence-associated alterations in multiple cardiac cell populations, disrupting cardiac homeostasis and contributing to pathological remodeling. In this review, we summarize current advances in DOX-induced cardiac senescence, focusing on the contributions of different cardiac cell types, the underlying molecular mechanisms, and emerging therapeutic strategies. We further discuss the challenges and future perspectives for developing effective interventions that alleviate cardiac senescence while preserving the anticancer efficacy of DOX. Understanding the mechanisms driving DOX-induced cardiac senescence may provide new opportunities to develop effective cardioprotective strategies and improve long-term cardiac outcomes after chemotherapy.

Biomolecules doi: 10.3390/biom16081179

Authors: Alyson Sato Nicole Chang Nebojsa Nick Knezevic Chanannait Paisansathan

Perioperative neurocognitive disorders (PND) encompass a spectrum of cognitive impairments occurring across the surgical period and are associated with significant morbidity, delayed recovery, and reduced quality of life. Although established risk factors include advanced age, cardiovascular disease, and preexisting cognitive impairment, the contribution of mood disorders to PND susceptibility remains incompletely understood. This review systematically examines the neurobiological overlap between mood disorders, particularly major depressive disorder (MDD) and bipolar disorder, and PND, with emphasis on shared biomolecular mechanisms. We identify convergent pathophysiologic pathways including hypothalamic–pituitary–adrenal (HPA) axis dysregulation, chronic neuroinflammation, NF-κB-mediated cytokine signaling, microglial priming, tryptophan–kynurenine pathway dysregulation, and brain-derived neurotrophic factor (BDNF) suppression. These mechanisms collectively suggest that patients with preexisting mood disorders may enter surgery in a biologically sensitized neuroimmune state, lowering the threshold for exaggerated neuroinflammatory responses and postoperative cognitive dysfunction. Recognition of mood disorders as modifiable perioperative vulnerability states may inform preoperative risk stratification, guide anesthetic and analgesic management, and support the development of targeted interventions to reduce postoperative cognitive complications and improve surgical outcomes.

Biomolecules doi: 10.3390/biom16081178

Authors: Inês Mansinhos Sandra Gonçalves Raquel Rodríguez-Solana Gema Pereira-Caro Anabela Romano

Mediterranean Lamiaceae species are important sources of bioactive compounds with potential applications in food, pharmaceutical, and cosmetic industries. In the present study, controlled salinity was evaluated as a biotechnological elicitation strategy to enhance the accumulation of bioactive metabolites in two species, Lavandula viridis and Thymus lotocephalus, cultured in vitro. Morphological, biochemical and metabolic responses of shoots grown for seven weeks in culture medium containing four NaCl concentrations (0, 25, 50, or 75 mM) were assessed. Mild salinity (25 mM NaCl) stimulated shoot growth in both species, whereas higher salt concentrations progressively reduced growth. Salinity induced oxidative stress, as indicated by elevated malondialdehyde (MDA) levels at 25 mM NaCl in both species, while hydrogen peroxide (H2O2) exhibited contrasting patterns, decreasing with increasing salinity in L. viridis but peaking at 50 mM NaCl in T. lotocephalus. Salt stress caused reductions in photosynthetic pigments, phenolic compounds, antioxidant capacity (DPPH, FRAP, ABTS, and ORAC), and overall metabolic performance in L. viridis, indicating limited tolerance to salinity. Conversely, T. lotocephalus displayed greater metabolic plasticity, characterized by increased levels of phenolic compounds, particularly rosmarinic acid and its derivatives, and higher antioxidant activity of the extracts, as well as the accumulation of proline and soluble sugars. These findings demonstrate marked species-specific differences in salinity responses and identify controlled salinity as an effective elicitation strategy to sustainably produce high-value bioactive compounds in T. lotocephalus.

Biomolecules doi: 10.3390/biom16081177

Authors: Kalisse I. Horne Joshua Chang Mell Chiaki Noguchi Sri Havya Jana Shriya Pinisetty Rhea Masand Christian Sell Eishi Noguchi

Timeless and its fission yeast ortholog Swi1 are evolutionarily conserved components of the replication fork protection complex that ensures faithful DNA replication and genome stability. While their nuclear roles are well-characterized, their roles in mitochondrial genome maintenance remain unknown. Here, we demonstrate a previously unrecognized connection between Timeless/Swi1 and mitochondrial homeostasis. In fission yeast, swi1 deletion increased association of the DNA repair protein Rad52 with mitochondrial DNA sequences across the mitochondrial genome, suggesting altered mitochondrial genome maintenance. Unexpectedly, swi1∆ cells showed an increased mtDNA copy number and improved growth under respiratory conditions, suggesting activation of compensatory mechanisms that promote mitochondrial genome maintenance. The loss of Swi1 also partially rescued the growth defect under respiratory conditions and mtDNA loss associated with depletion of mitochondrial DNA polymerase γ, linking Swi1 to pathways regulating mitochondrial replication under stress. Consistent with these phenotypes, transcriptomic and pathway enrichment analyses revealed transcriptional changes indicative of reduced glycolysis and enhanced oxidative phosphorylation, suggesting a shift toward respiratory metabolism. In human cells, Timeless depletion elicited distinct mitochondrial responses depending on the cell type. While Timeless-depleted TE-11 and Saos-2 cells elicited mitochondrial phenotypes comparable to those observed in fission yeast, Timeless depletion in U-2 OS cells led to reduced mtDNA copy number, elevated mitochondrial reactive oxygen species, and decreased mitochondrial membrane potential and mass, consistent with mitochondrial dysfunction. Despite these phenotypic differences, both fission yeast and human cells exhibited elevated levels of orthologs of the mitochondrial transcription factor A (TFAM) and the oxidative stress regulator NRF2, suggesting the conserved activation of compensatory mitochondrial and antioxidant pathways. Together, these findings identify an evolutionarily conserved connection between Timeless/Swi1 and mitochondrial homeostasis and reveal distinct adaptive responses to mitochondrial stress.

Biomolecules doi: 10.3390/biom16081176

Authors: Qi Huang Shuguang Wang Yuman Huang Shibo Xiao Ruohan Xia Xianwang Wang

Pulmonary fibrosis is a progressive interstitial lung disease characterized by persistent alveolar epithelial injury, aberrant repair, and excessive extracellular matrix deposition. Increasing evidence indicates that disease progression is closely associated with alveolar type II (AT2) cell dysfunction, impaired AT2-to-AT1 differentiation, and the persistence of transitional epithelial populations, including KRT8+ intermediate populations. Because the formation and resolution of these transitional epithelial populations require dynamic regulation of stress-responsive transcripts and differentiation-associated RNA programs, they provide a biologically relevant context for investigating RNA modification-mediated post-transcriptional regulation. RNA modifications have emerged as post-transcriptional regulatory layers that modulate RNA stability, processing, translation efficiency, and stress-response gene expression, thereby influencing epithelial stress adaptation and repair-related state transitions. Among these modifications, N6-methyladenosine (m6A) is the best-characterized layer, with evidence linking it to epithelial injury responses, senescence-associated transcript remodeling, and differentiation impairment. In contrast, non-m6A modifications, including m5C, m1A, m7G, pseudouridine (Ψ), and A-to-I RNA editing, remain emerging regulatory layers with limited AT2 cell-specific functional validation. This review summarizes current evidence connecting RNA modifications with alveolar epithelial injury, transitional-state persistence, epithelial–mesenchymal communication, and fibrotic remodeling. Rather than interpreting RNA modifications as isolated pathogenic drivers, we highlight their context-dependent roles in RNA fate control, epithelial stress adaptation, and aberrant repair in pulmonary fibrosis.

Biomolecules doi: 10.3390/biom16081174

Authors: Tingting Liu Quanye Luo Shihong Yang Dongmei Yang Xuzhen Lv Liyan Zhao Qinhui Tuo

Objectives: Endothelial apoptosis is a central event in atherosclerotic vascular injury, yet the contribution of the INO80 chromatin-remodeling subunit INO80E to this process remains unclear. This study examined whether INO80E is altered during atherosclerosis (AS)-associated endothelial injury and explored its functional role in ox-LDL-triggered apoptosis. Methods: Atherosclerotic mouse models were used to examine INO80E expression in vascular tissues, and ox-LDL-treated HUVECs were applied as an in vitro model of endothelial injury. The functional role of INO80E was evaluated using lentiviral overexpression and siRNA-mediated knockdown approaches, while apoptosis was measured by flow cytometry and TUNEL staining. Mechanistic experiments included co-immunoprecipitation, immunofluorescence, YY1 acetylation analysis, and pharmacological inhibition with the pan-HDAC inhibitor trichostatin A (TSA). In addition, YY1-silencing rescue experiments were performed in INO80E-overexpressing cells to determine whether YY1 contributes to the protective effect of INO80E against ox-LDL-induced endothelial apoptosis. Results: INO80E expression was reduced in the endothelial layer of ApoE−/− aortas and in ox-LDL-treated HUVECs. INO80E overexpression attenuated ox-LDL-induced apoptosis and increased the Bcl-2/BAX ratio, whereas INO80E knockdown produced the opposite effect. INO80E colocalized with HDAC1, increased the HDAC1-YY1 association, decreased YY1 acetylation, and prolonged YY1 protein stability. TSA treatment weakened the anti-apoptotic phenotype associated with INO80E overexpression, and rescue experiments showed that YY1 knockdown partially reversed the INO80E overexpression-associated regulation of Bcl-2 and BAX. Conclusions: These findings suggest that INO80E protects endothelial cells from ox-LDL-induced apoptosis, at least in part by promoting HDAC-associated YY1 deacetylation and stabilization. The INO80E-HDAC1-YY1 pathway may represent a candidate protective mechanism in AS that requires further validation.

Biomolecules doi: 10.3390/biom16081175

Authors: Maria A. Katsianou Eleni-Kyriaki Vetsika Mariam Markouli Christina Piperi Antonios N. Gargalionis

Brain aging is characterized by extensive and dynamic epigenetic changes that reshape chromatin architecture and influence gene regulatory networks, leading to deregulation of transcriptional programs essential for neuronal survival, synaptic plasticity, and cognitive function. Emerging studies highlight the pivotal regulatory role of the Polycomb Repressive Complex 2 (PRC2) in brain aging, functioning mainly as an epigenetic silencer through the establishment of the H3K27me3 histone mark at gene promoters and enhancers, leading to transcriptional repression. Altered distribution and decreased activity of PRC2 during aging disrupts the balance between gene activation and repression, affecting pathways involved in neurogenesis, synaptic plasticity and stress response. Further interplay with other epigenetic regulators such as histone deacetylase 2 (HDAC2), DNA methyltransferases and non-coding RNAs forms an extensive network that contributes to cognitive decline, increasing vulnerability for neurodegeneration. In this review, we describe structural and functional aspects of PRC2, with emphasis on the potential of this epigenetic context-dependent regulator to integrate developmental, environmental and aging-related signals, to shape the transcriptional landscape of aging brain. We also discuss the newly developed PRC2-AgeIndex, which serves as a prognostic biomarker for age-related neurodegeneration and monitoring treatment response, as well as current PRC2-targeting options for healthy brain aging.

Biomolecules doi: 10.3390/biom16081173

Authors: Igor A. Schepetkin Alexander V. Uvarov Egor A. Evriinov Andrei I. Khlebnikov

Indolo[2,3-b]quinoxalines, along with their N-substituted derivatives, exhibit pronounced anticancer activity, although the mechanisms of their biological action may vary. Herein, a panel of sixty-five 6-(2-aminoethyl)-6H-indolo[2,3-b]quinoxaline derivatives comprising eight series with distinct amine moieties connected to the tetracyclic indoloquinoxaline core via a dimethylene linker was evaluated as drug-like candidates for kinase binding and cytotoxic activity. The ADME (Absorption, Distribution, Metabolism, and Excretion) properties of the compounds included in this set were preliminarily determined using the SwissADME tool. Analysis revealed that the library of quinoxaline derivatives largely complies with the drug-likeness rule for kinase-targeted compounds. As part of the biological screening, the compounds were initially tested on two cell lines MonoMac-6 and THP-1 (both derived from patients with acute monocytic leukemia) using sunitinib, a known antitumor agent acting as a multi-target receptor tyrosine kinase inhibitor, as a reference compound. Compound 3g, which demonstrated the highest activity in the cytotoxicity analysis (IC50 = 1.9 and 3.5 μM for the MonoMac-6 and THP-1 cell lines, respectively), was screened using the Eurofins DiscoverX scanEDGE panel, comprising 97 distinct kinases representing all known kinase families. Subsequently, the compound was tested using the Eurofins DiscoverX scanTK™ panel, covering 135 distinct receptor and non-receptor tyrosine kinases. Based on initial screening results, compound 3g exhibits relatively high binding activity against fourteen tyrosine kinases, including TYK2, ZAP70, eight mutant forms of ABL1, two mutant forms of FLT3, and one mutant form of ALK, and demonstrates relatively high binding selectivity with respect to non-mutant tyrosine kinases (S-score: 0.024). Secondary screening of nine selected analogs of compound 3g led to the identification of compound 3h, which demonstrates relatively high binding affinity for FLT3 (D835V) (Kd = 0.41 μM). Molecular modeling suggested modes of binding interaction of the compounds 3h and 3g in the FLT3 (D835V) catalytic site. Our results demonstrate that 6-(2-aminoethyl)-6H-indolo[2,3-b]quinoxaline derivatives could be potential candidates for developing anticancer drugs.

Biomolecules doi: 10.3390/biom16081172

Authors: Tyler J. Woodward Brittany M. Ripley Justin A. Ling M. Todd Washington

Translesion synthesis is a major DNA damage bypass pathway in which specialized DNA polymerases, such as pol η and Rev1, are recruited to stalled replication forks where they catalyze nucleotide incorporation opposite DNA damage. Translesion synthesis is regulated by the Rad6-Rad18 complex, which catalyzes PCNA mono-ubiquitylation. Despite its central role in regulating translesion synthesis, its oligomeric state and molecular interactions are poorly understood. Here, we use mass photometry to show that Rad18 co-purifies with Rad6 and forms a series of larger oligomeric complexes. Using yeast two-hybrid studies, we showed that while the full-length Rad18 complex interacts with pol η, its interaction with Rev1 is controlled by auto-inhibition. The release of this auto-inhibition is associated with the dissociation of the Rad6-Rad18 complex, freeing Rad18 monomers and dimers. Because pol η participates in non-mutagenic translesion synthesis, while Rev1 participates in mutagenic translesion synthesis, this auto-inhibition likely allows pol η preferential access to stalled replication forks by delaying Rev1 recruitment. Such an ordered polymerase-recruitment mechanism would reduce the likelihood of mutations.

Biomolecules doi: 10.3390/biom16081171

Authors: Sicheng Yan Xinjia Li Yu Yuan Yongjie Yang Xuewen Tian Xi Chen Lan Zhang Shihua Zhang

Bone remodeling imbalance represents the fundamental pathological basis of osteoporosis. Exercise is broadly regarded as a valuable non-pharmacological strategy for preventing and managing osteoporosis; however, the precise molecular mechanisms through which exercise modulates bone metabolism remain incompletely understood. Mitophagy has recently been recognized as an important mediator linking exercise to the regulation of bone remodeling. This review centers on the “exercise–mitophagy–bone remodeling” axis, systematically outlining the biological processes and regulatory determinants of mitophagy within the bone microenvironment. Evidence suggests that mitophagy facilitates bone formation by preserving mitochondrial quality, attenuating oxidative stress, and optimizing cellular energy metabolism. Moreover, it exerts stage-specific inhibitory effects on bone resorption during osteoclast differentiation. Particular emphasis is placed on the mechanisms by which exercise activates mitophagy-related signaling pathways via metabolic, mechanical, and hypoxic stimuli. In addition, exercise may enhance the efficiency of this regulatory axis by maintaining vitamin D and calcium homeostasis and modulating estrogen signaling pathways. The differential effects of exercise modalities and durations on these processes are also critically evaluated. Finally, this review addresses current limitations in existing research and highlights future directions, including the optimization of exercise interventions targeting mitophagy and the integration of multi-omics approaches. These findings offer a theoretical basis for designing precise exercise regimens and combined therapeutic approaches in the management of osteoporosis.

Biomolecules doi: 10.3390/biom16081170

Authors: Camilla Di Meo Sakthimala Palaniappan Cristina Urbano Giacomo Cimino Francesco Cestra Noemi De Dominicis Veronica Carnicelli Annamaria Tisi Mauro Maccarrone

Endogenous bioactive lipids are complex signaling mediators actively involved in a plethora of pathophysiological processes, including energy homeostasis and fibrosis. Energy homeostasis is a stable internal state resulting from a dynamic balance between energy expenditure and storage. Dysregulated energy balance can contribute to fibrosis, exhibiting key metabolic effects on insulin sensitivity, glucose tolerance, lipid accumulation and metabolism, as well as on energy expenditure, ultimately leading to metabolic disorders. In this context, three major classes of endogenous lipid mediators derived from polyunsaturated fatty acids (PUFAs)—eicosanoids, specialized pro-resolving mediators, and endocannabinoids—represent a key signaling network involved in the regulation of energy metabolism. Hence, alterations in their metabolism and signaling are often associated with fibrosis and other related molecular changes. Here, we provide a comprehensive overview of the role of the above-mentioned lipid classes in energy homeostasis and fibrosis by reviewing the available literature spanning nearly four decades, with a primary focus on studies published over the past 20 years.

Biomolecules doi: 10.3390/biom16081169

Authors: Sisi Zhao Luxi Cao Feidan Deng Zhenge Liao Xiaoxiang Li Guanglei Li Chunzhi Tang Yimin Zhang Shujun Lin

(1) Background: Traumatic brain injury (TBI) triggers synaptic loss, leading to long-term neurological deficits. Electroacupuncture (EA) benefits neurological conditions, but its mechanisms after TBI remain unclear. (2) Methods: We used a controlled cortical impact (CCI) mouse model. Behavioral outcomes were assessed using the modified neurological severity score (mNSS), rotarod, Y-maze, and novel object recognition test (NORT). Synaptic morphology was examined by transmission electron microscopy (TEM). Energy metabolism was assessed using biochemical assays, and mitochondrial function was assessed using flow cytometry. Quantitative real-time PCR (qPCR) and Western blotting (WB) were used to examine the underlying molecular mechanisms. (3) Results: We found that EA ameliorates TBI-induced motor and cognitive impairments by preserving synaptic and mitochondrial integrity. EA-treated mice showed improvements in mNSS, rotarod, NORT, and Y-maze performance, along with preserved synaptic ultrastructure and mitochondrial function. CaMKII overexpression abolished EA-induced neuroprotection, identifying the CaMKII/Drp1 axis as a key mediator. (4) Conclusions: Thus, EA limits TBI deficits by restraining CaMKII/Drp1-driven mitochondrial fission and subsequent synaptic loss.

Biomolecules doi: 10.3390/biom16081168

Authors: Dezhi Yang Qingmei Hu Feng Shi Xueling Chen Yiquan Lin Cuihua Fu Fang Zhao Xiaoju Zou Xiaoxu Bi Zichao Liu

Hyperlipidemia (HL) is a major metabolic disorder and a critical risk factor for cardiovascular diseases, closely associated with oxidative stress, inflammation, and disrupted cholesterol homeostasis. Freeze-dried Poecilobdella manillensis powder (FDPMP), a traditional medicinal product, has shown therapeutic potential against hyperlipidemia; however, its underlying mechanisms remain largely unclear. In this study, HL was induced in ApoE−/− mice by feeding a high-fat diet (HFD) for eight weeks, during which FDPMP or simvastatin (positive control) was orally administered daily. Concurrently, an in vitro foam cell model was established by exposing RAW264.7 macrophages to oxidized low-density lipoprotein (ox-LDL, 80 μg/mL) for 24 h, with FDPMP pretreatment applied 30 min prior to ox-LDL stimulation. Following intervention, serum lipid profiles, hepatic oxidative stress markers, histopathological changes, and cholesterol metabolism-related gene and protein expression were systematically evaluated. FDPMP administration significantly improved serum lipid profiles by reducing triglycerides, total cholesterol, and low-density lipoprotein cholesterol, while increasing high-density lipoprotein cholesterol levels. Additionally, FDPMP alleviated histopathological damage in the liver, kidney, and heart, enhanced antioxidant enzyme activities, and attenuated oxidative stress. Untargeted metabolomic analysis revealed that FDPMP markedly modulated key metabolic pathways, including choline metabolism, glycerophospholipid metabolism, and arachidonic acid metabolism. Mechanistically, FDPMP restored cholesterol homeostasis through dual regulation of cholesterol metabolism, characterized by upregulation of cholesterol 7α-hydroxylase (CYP7A1) to promote bile acid-mediated cholesterol excretion, alongside downregulation of 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) and synthase (HMGCS1) to inhibit cholesterol biosynthesis. In vitro, FDPMP effectively suppressed ox-LDL-induced foam cell formation, reduced intracellular lipid accumulation, and mitigated oxidative stress in macrophages. Collectively, these findings demonstrate that FDPMP ameliorates hyperlipidemia through coordinated regulation of cholesterol synthesis and excretion, coupled with systemic metabolic reprogramming and antioxidative effects. This study provides mechanistic insights supporting FDPMP as a promising natural therapeutic candidate for hyperlipidemia and related metabolic disorders.

Biomolecules doi: 10.3390/biom16081167

Authors: Samhita Kotapati Meenakkshy Manoharan Emanuela Palmerini

Primary bone sarcomas are rare, heterogeneous malignancies with limited therapeutic options, particularly in metastatic disease where outcomes remain poor. This study synthesizes current literature to evaluate emerging therapeutic strategies and biological determinants of response across osteosarcoma, Ewing sarcoma, and chondrosarcoma, as presented at the ESMO Annual Meeting, 2025. Key approaches reviewed include VEGFR-targeted tyrosine kinase inhibitors (TKIs), DNA damage response (DDR) inhibition, MYC targeting, immune checkpoint inhibitors (ICIs), and surfaceome-directed therapies such as antibody–drug conjugates (ADCs) and chimeric antigen receptor T cell therapy. Across studies, TKIs demonstrated short lasting activity as monotherapy but improved outcomes in some of the studies when combined with ICIs or chemotherapy, reflecting their role in remodeling the tumor microenvironment (TME); importantly, controlled studies with TKI and chemotherapy upfront are ongoing. DDR- and MYC-targeted therapies have shown strong preclinical rationale but limited clinical efficacy, highlighting challenges in translation. Immune-based therapies exhibited variable responses, with dedifferentiated chondrosarcoma (DDCS) emerging as a responsive histotype. Surfaceome-targeting strategies, particularly ADCs, demonstrated promising early clinical activity. Overall, bone sarcoma rarity, tumor heterogeneity, immunosuppressive TME, and lack of predictive factors challenge drug discovery for bone sarcoma patients. These findings underscore the importance of combination strategies and biomarker-driven patient selection and suggest that continued integration of targeted and immunotherapeutic approaches will be critical to improving outcomes in bone sarcoma.

Biomolecules doi: 10.3390/biom16081166

Authors: Ana G. Castillo-Olmos Abigail Varela-Pérez Hugo S. García-Galindo Joaquín A. Quiroz-Mercado Kimberly Castañeda-Gutiérrez Carlos Amero Enrique Rudiño-Piñera Mizraim Morales-Mendoza Cynthia Cano-Sarmiento

Cataracts are the leading cause of reversible blindness worldwide; this condition results from the aggregation of lens proteins. Currently, surgery remains the only treatment; however, there is growing interest in non-surgical approaches, including the use of bioactive compounds incorporated into nanostructured systems designed to enhance solubility, enable controlled release, and improve bioavailability and bioactivity. Among the bioactive compounds investigated, curcumin has attracted considerable attention due to its antioxidant and anti-inflammatory properties, positioning it as a potential anticataractogenic agent. In the present study, curcumin-loaded nanoemulsion was developed via ultrasonication and characterized by average particle size, D90 percentile, ζ potential, and rheological behavior. In addition, its anti-cataract efficacy was evaluated both using an in vivo model in rats and an ex vivo model employing human cataract samples. The resulting curcumin-loaded nanoemulsion exhibited an average particle size of 152 ± 19.79 nm with a monomodal distribution, along with good physical stability over time. The nanoemulsion exhibited apparent viscosity between 30 and 25 mPa·s, at shear rate values (100 to 0 s−1), indicating slight shear-thinning behavior. Regarding the effect on cataracts, in the in vivo model, cataract reversal was observed. Furthermore, ex vivo isothermal titration calorimetry (ITC) analyses indicated exothermic heat exchange between the curcumin nanoemulsions and cataract fragments, consistent with binding interactions occurring within lens components, likely involving crystallin proteins. These findings provide biophysical and in vivo evidence that intravitreally administered curcumin-loaded nanoemulsions not only prevent but actively reverse lens opacity, positioning them as a promising non-surgical therapeutic approach for cataract treatment.

Biomolecules doi: 10.3390/biom16081165

Authors: Chandrasekharam N. Nagineni Rajani Choudhuri Murali C. Krishna James B. Mitchell

We investigated the effects of senescence and hypoxia on the transcriptome and secretome of the colon cancer cell, HCT-116, in an in vitro model. Senescence was confirmed using SA-β Gal staining and the expression of p53 and p21 proteins, and hypoxia using HIF-1α protein. Control (CN) and senescent (SN) cells were exposed to normoxia or hypoxia, control hypoxia (CH), and senescent hypoxia (SH). Senescence (SN, SH) enhanced the expression of kallikrein-related peptidases, TPp53, p21, optineurin, lipocalin, ADH-1, and stratifin by several folds. Stratifin, with tumor suppressive functions, was upregulated in senescent cells under normoxia but not in hypoxia. Hypoxia (CH and SH) upregulated the expression of many glycolysis genes, especially HK, PFK, aldolase, PDH kinase, and LDH-A. Mitochondrial RNAs (tRNA and rRNA) were increased in SH compared to CH. Significant increases in the secretion of IL-1α, endothelin, bFGF, HB-EGF, PDGF-AB, CCL-5, 7, 22, and CXCL-1 and 8 were observed in SN and SH. VEGF-A, VEGF-C, and TNF-β secretion increased, while PLGF, TGF-α, IL-27, GM-CSF, and M-CSF decreased under hypoxic (CH and SH) conditions. Thus, senescence and hypoxia contribute to cancer cell senescence pathophysiology by regulating the cellular transcriptome and secretome and by both positive and negative feedback mechanisms.

Biomolecules doi: 10.3390/biom16081164

Authors: Bartosz Rodziewicz Mikołaj Kacperski Kacper Kisiński Marta Zawadzka Anna Kalicka Agnieszka Sawicka Beata Lipska-Ziętkiewicz Maria Mazurkiewicz-Bełdzińska

Loss-of-function (LoF) variants in the PRPS1 gene, encoding the phosphoribosyl pyrophosphate (PRPP) synthetase 1 enzyme, cause rare neurometabolic disorders historically viewed as discrete entities: nonsyndromic deafness (DFNX1), Charcot–Marie–Tooth disease type X5 (CMTX5), and Arts syndrome. A major clinical challenge is the temporal dissociation between early auditory failure and subsequent neurodegeneration, causing fragmented diagnostics. We systematically quantified this diagnostic latency and reconceptualized the disease spectrum through a molecular lens. A PRISMA-compliant systematic review identified 19 patients with genetically confirmed PRPS1 LoF variants, including our index case (c.362C>G) presenting a 15-year diagnostic delay. Kaplan–Meier analysis revealed sensorineural hearing loss manifested acutely (median 0 years; 95% CI: 0–1). In contrast, neurological deficits demonstrated a prolonged latency (median 3 years; 95% CI: 1–8), followed by ophthalmological signs (median 11.5 years). The median symptomatic delay was 3 years (range up to 19). We posit that this temporal dissociation reflects differential tissue vulnerability to intracellular ATP/GTP and NAD+ depletion caused by the primary enzymatic defect. Ultimately, DFNX1, CMTX5, and Arts syndrome represent a continuous PRPS1-related neurometabolic spectrum. Because targeted metabolic interventions (such as S-adenosylmethionine or nicotinamide riboside) have limited efficacy on advanced structural nerve damage, recognizing this early diagnostic window to initiate biochemical rescue prior to irreversible axonal degeneration is critical.

Biomolecules doi: 10.3390/biom16081163

Authors: Lingyuan Ma Li Sun Haotian Zhang Chuanying Pan Mingxun Li Xianyong Lan Yang Li

The genetic and physiological variations among individuals of Holstein dairy cattle contribute to variations in milk yield. Selecting high-yield cows is critical for improving lactation performance. The present study aimed to identify functional genetic variants of the 3′ untranslated region (3′ UTR) in the ELF5 gene associated with milk production traits and to elucidate their underlying molecular mechanisms. A total of 1314 Chinese Holstein cows were genotyped, and a novel single nucleotide polymorphism (SNP), ELF5 g.32793 G>T, was identified in the 3′ UTR of ELF5. This SNP was significantly associated with milk production, such as milk yield, milk fat percentage, milk protein percentage, and somatic cell score. Bioinformatic prediction and dual-luciferase reporter assays demonstrated that the ELF5 g.32793 G>T affects the interaction between bta-miR-487a and the ELF5 3′ UTR. Functional analyses in bovine mammary epithelial (MAC-T) cells showed that bta-miR-487a suppressed cell proliferation by inducing G0/G1 phase arrest and reduced the expression of proliferation-related proteins. Collectively, these findings suggested that bta-miR-487a participates in the regulation of MAC-T cell growth and that the ELF5 g.32793 G>T polymorphism may influence lactation performance through an miRNA-associated mechanism. Therefore, the variant can be used as a functional marker for marker-assisted selection in dairy cattle breeding.

Biomolecules doi: 10.3390/biom16081162

Authors: Menghan Li Bin Zhang Youyan Zeng Yongxin Mao Jinyi Zhang Tingfang Zhao Huanglin Huo Huicong Zeng Qian Zhou Bo Li

Efficient treatment of diabetic wounds (DW) remains a major clinical challenge worldwide owing to vascular insufficiency, multiple bacterial infections, and overactivation of pro-inflammatory M1 macrophages caused by hyperglycemia. The development of novel pharmaceutical agents with multiple biological functions is urgently needed. Coptis chinensis Franch. (CC) has been used to treat diabetes for thousands of years in China, but the curative effects and underlying mechanisms of CC in DW remain uncertain. Herein, a homogeneous heteropolysaccharide component, namely CCP, was isolated and purified from CC, which exhibited a molecular weight of 39,697 Da and was primarily composed of Glc, GalA, Ara, Gal, and Xyl. CCP has a light yellowish color and is distributed in a block shape with small surface granulations. In vitro experiments revealed that CCP dose-dependently mitigated high glucose-induced suppression of viability, migration, and tube formation in HUVECs. Meanwhile, CCP promotes the polarization of M1 macrophages toward the M2 phenotype to exert anti-inflammatory effects, while possessing certain antibacterial properties. In addition, a composite hydrogel system was successfully constructed by introducing sodium carboxymethyl cellulose and carbomer 940 for CCP delivery. The obtained hydrogels exhibited reasonable moisturizing, swelling, and drug release capacities, along with favorable rheological behaviors and certain antibacterial activity. More importantly, the in vivo wound healing model evaluation in diabetic rats demonstrated that CCP hydrogel dressings could effectively promote wound healing by reducing inflammation, accelerating collagen deposition, upregulating the expression of VEGF and key angiogenesis-related factors. In addition, composite hydrogels demonstrated excellent cytocompatibility and hemocompatibility, which holds great promise for clinical application in DW treatment.

Biomolecules doi: 10.3390/biom16081161

Authors: Luoyi Chen Qiang Zhang Yizhong Tu Tong Chen Yunliang Xie Kaixin Lan Wei Yan Chunyuan Xue Shuangjin Yu Jiang Qiu

Chronic kidney disease (CKD), one of the major global public health burdens, continues to exhibit a rising prevalence worldwide. The growing population of patients with end-stage renal disease (ESRD) has led to an increasing demand for renal replacement therapy (RRT). Although dialysis effectively prolongs survival, it fails to fully replicate kidney function. In addition, the persistent shortage of donor kidneys results in prolonged waiting periods for kidney transplantation. Emerging renal replacement strategies, such as kidney organoids, have demonstrated considerable potential. However, multiple technical limitations continue to hinder their near-term clinical translation. Bioartificial kidneys (BAKs), which integrate engineering and biological technologies, generally consist of artificial filtration membranes and living-cell bioreactors designed to mimic native kidney function. Advances in nanotechnology, biomaterials, and tissue engineering have accelerated the development of implantable bioartificial kidneys (iBAKs), making them an important research direction in renal replacement therapy. These innovations have improved membrane performance, biocompatibility, and cellular integration; however, substantial challenges remain regarding long-term stability, immune compatibility, and clinical validation before translation into human applications. Specifically, limited cell sources and uncertain long-term biocompatibility remain major barriers to iBAK development. In the future, biosensors and artificial intelligence (AI) technologies may be incorporated into bioartificial kidneys to enable personalized precision therapy. This review focuses on the developmental and major challenges of bioartificial kidneys, with detailed discussion of recent progress in implantable artificial kidneys.

Biomolecules doi: 10.3390/biom16081160

Authors: Nayra Oliveira Prado Anelis Maria Marin Carolina Zem Micheli de Marchi Diogo Dias Araújo Maria José Ferreira Alves Miyuki Uno Roger Chammas Dalila Lucíola Zanette Mateus Nóbrega Aoki

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers worldwide, largely because it is diagnosed late. Diagnosis typically relies on imaging and biopsy, but only after tumors have advanced, which reduces treatment effectiveness. Current biochemical biomarkers are limited to CA19-9, which is more useful for prognosis and monitoring than for diagnosis. Circulating miRNAs may offer minimally invasive complementary biomarkers for PDAC diagnosis, potentially accounting for ethnic and treatment-related variables. We performed small RNA sequencing on plasma from five non-metastatic-stage and five metastatic-stage PDAC patients and 10 healthy controls to generate an exploratory miRNA profile. Candidate miRNAs were then validated by RT-qPCR in an independent cohort of 70 PDAC patients and 106 healthy controls, and nine miRNAs showed promising differential plasma expression. Notably, miRNA484 and miRNA335-5p were associated with PDAC in CA19-9-negative patients, with ROC AUCs of 0.984 and 0.88, respectively. Overall, these results indicate that miRNA484 and miRNA335-5p may have clinical value as complementary biomarkers for PDAC patients who are CA19-9-negative.

Biomolecules doi: 10.3390/biom16081159

Authors: Anastasiia Filimonova Dieter Spiteller

In contrast to honeybees, the Australian stingless bee Tetragonula carbonaria appears to be robust against microbial pathogens. Streptomyces sp. 127Q, isolated from T. carbonaria, inhibited the growth of Lysinibacillus sphaericus, which is the only microorganism reported to affect T. carbonaria. The antimicrobials were purified from Streptomyces sp. 127Q by bioassay-guided isolation using ethyl acetate extraction and Diaion HP20 chromatography, followed by reverse phase HPLC fractionation. The antimicrobial compounds were identified by high-resolution mass spectrometry, UV-Vis-spectroscopy, nuclear magnetic resonance spectroscopy, and genome mining as new members of the trioxacarcin/gutingimycin family having a 1,2-dihydroxyanthraquinone aromatic core structure. A closely related gutingimycin with a 1,2-dihydroxyanthraquinone moiety was previously observed in a crystallisation experiment of trioxacarcin A with an oligonucleotide. Streptomyces sp. 127Q produces a wide range of trioxacarcins/gutingimycins. At the onset of trioxacarcins production, Streptomyces sp. 127Q appeared to rapidly convert trioxacarcin epoxides with water, guanine, and nicotinic acid. The 1,2-dihydroxyanthraquinone trioxacarcins, trioxacarcin 692 and trioxacarcin 780, inhibited L. sphaericus with minimal inhibitory concentrations (MICs) of 37.5 μM and 75 μM, respectively. The MIC against Escherichia coli and Staphylococcus aureus was 75 μM and 150 μM, respectively. In the photoantimicrobial screening, the MIC for trioxacarcin 692 against E. coli and S. aureus decreased by 8-fold, and for trioxacarcin 780 by 4-fold. Following light pretreatment, trioxacarcin 692 (9.4 μM) inhibited E. coli and S. aureus at concentrations comparable to those of the established antibiotics ciprofloxacin and vancomycin. Neisseria gonorrhoeae was only inhibited at an MIC of ca. 18.8 μM after light preincubation. The 1,2-dihydroxyanthraquinone trioxacarcins constitute powerful antimicrobial compounds belonging to the trioxacarcin/gutingimycin family.

Biomolecules doi: 10.3390/biom16081158

Authors: Zenghua Sheng Qiaoyun Fang Siqian Cui Jian Wang Huihui Xiao Chunrong Wu Debing Xiang

Among primary central nervous system malignancies in adults, malignant glioma ranks first in incidence, with glioblastoma (GBM) standing as its most aggressive phenotype. This malignancy remains a devastating disease with limited therapeutic options, largely owing to the intricate network of dysregulated signaling pathways. SUMOylation, a post-translational modification that governs thousands of substrate proteins, is markedly hyperactivated in GBM and represents a rational but underexploited target. Here, we found that honokiol (HNK), a natural biphenolic compound extracted from the traditional Chinese medicine Magnolia species, suppressed SUMOylation in glioma cells, with a more prominent reduction in SUMO1-conjugated species than in SUMO2/3-conjugated species. Through a combination of label-free proteomic screening and functional biological assays, we pinpointed YAP1, a core Hippo pathway effector and established oncogenic driver in glioma cells, as a critical downstream target. Furthermore, our research indicated that inhibition of SUMOylation by HNK was associated with reduced levels of YAP1, resulting in glioma cell growth inhibition. Mechanistically, HNK induced YAP1 ubiquitin–proteasome degradation by disrupting SUMO1-YAP1 conjugation, leading to the subsequent blockade of YAP1 signaling. Collectively, our findings unveiled a previously unrecognized mechanism linking pharmacological deSUMOylation to YAP1 destabilization and emphasized the SUMO–YAP1 interface as a therapeutically actionable vulnerability. Overall, this work provides a strong rationale for developing HNK or its optimized derivatives as a first-in-class therapeutic strategy that addresses the network-level complexity of GBM.

Biomolecules doi: 10.3390/biom16081157

Authors: Ying Wang Wenyu Wu Wudi Wang Weichang Li Zhenggang Yue Chengbang Ma Lei Wang Mei Zhou James F. Burrows Tianbao Chen Fanxing Xu

Impaired endothelial function, excessive oxidative stress, and persistent bacterial infection collectively contribute to delayed healing of diabetic chronic wounds. Methylglyoxal (MGO)-induced metabolic stress is a critical driver of endothelial injury; however, effective multifunctional strategies capable of restoring vascular function and maintaining cellular homeostasis remain limited. In this study, the endothelial protective potential of an amphibian-derived Bowman–Birk inhibitor (BBI)-type peptide, OSTI-1872, and its rationally designed structural analogues were investigated using an MGO-induced injury model in human umbilical vein endothelial cells (HUVECs). Among the tested peptides, the optimised analogue OSTI-2337 exhibited superior protective activity. OSTI-2337 markedly attenuated MGO-induced oxidative stress, restored nitric oxide bioavailability, enhanced VEGF expression, promoted endothelial migration and tube formation, and reduced oxidative DNA damage. Mechanistically, these effects were associated with coordinated regulation of MGO detoxification and redox homeostasis, as evidenced by enhanced GLO1 expression and modulation of the PI3K/AKT/GSK3β/Nrf2 axis, accompanied by increased expression of downstream antioxidant proteins HO-1 and NQO1. In addition, OSTI-1872 and OSTI-2337 displayed antibacterial activity against representative bacterial strains, suggesting their potential advantages for complex diabetic wound environments. Collectively, these findings demonstrate that structural optimisation significantly enhances the biological activity of amphibian BBI-type peptides and identify OSTI-2337 as a multifunctional peptide candidate capable of integrating endothelial protection, MGO detoxification, redox regulation, and antibacterial activity for the management of diabetes-associated vascular injury and chronic wound complications.

Biomolecules doi: 10.3390/biom16081156

Authors: Rafael Fernandez Asha Jacob Monowar Aziz Ping Wang

Enolase-1 (ENO-1) is classically known as a highly conserved glycolytic enzyme that catalyzes the conversion of 2-phosphoglycerate to phosphoenolpyruvate in the final steps of glycolysis. This enzyme, however, is being increasingly implicated as a multifunctional moonlighting protein with compartment-specific roles in inflammation. Within the cytosol, ENO-1 regulates macrophage inflammation during sepsis; on the cell surface, it functions as a plasminogen receptor, and extracellularly, it can participate in innate immune signaling. Across innate and adaptive immunity, ENO-1 has been implicated in macrophage activation, neutrophil recruitment, endothelial cell dysfunction, fibroblast remodeling, and autoantigenicity. These functions have been linked to sepsis, acute respiratory distress syndrome, acute organ injury, hemorrhagic shock, rheumatoid arthritis, and cancer-associated inflammation in the tumor microenvironment. Therapeutic targeting of ENO-1 includes small-molecule inhibitors and monoclonal antibodies. ENO-1, with its compartment-specific functions in disease pathogenesis, serves as a significant therapeutic target for inflammatory diseases. In this review, we discuss the novel compartment-specific roles of ENO-1 in inflammatory diseases, defining its functions beyond its role in glycolysis. We conclude that both the metabolic and moonlighting functions of ENO-1 contribute to inflammation, and future studies should delineate its compartment-specific roles in inflammatory pathophysiology, as compartment-specific targeting may represent the future of ENO-1-directed therapy.