Biomolecules

14 pages, 2068 KB

Open AccessCommunication

Epitranscriptomic Stability—Variable Extents of N1-Methyladenosine to N6-Methyladenosine Conversion Under Different Experimental Conditions

by Frank Morales Shnaider, Hasna Kanan, Shrikant Patel and Norman H. L. Chiu

Biomolecules 2026, 16(5), 712; https://doi.org/10.3390/biom16050712 (registering DOI) - 12 May 2026

Abstract

The growing interest in epitranscriptomes has emphasized the need for accurate quantification of RNA modifications. However, the stability of RNA modifications under different experimental conditions remains poorly characterized. In this study, we use N1-methyladenosine (m¹A) as a model for assessing stability. [...] Read more.

The growing interest in epitranscriptomes has emphasized the need for accurate quantification of RNA modifications. However, the stability of RNA modifications under different experimental conditions remains poorly characterized. In this study, we use N1-methyladenosine (m¹A) as a model for assessing stability. After exposing m¹A ribonucleoside to various conditions that are commonly used in RNA protocols, the sample was analyzed using untargeted high-resolution mass spectrometry. Under alkaline or neutral pH, different extents of m¹A were converted to N6-methyladenosine (m⁶A). Complete m¹A-to-m⁶A conversion occurred at elevated temperatures. The m¹A-to-m⁶A conversion was also dependent on the initial m¹A concentration; the higher the concentration, the higher the rate of conversion. This poses a challenge to comparative studies if the initial amount of m¹A in the control and sample of interest are not equal. No demethylation or depurination was detected. However, trace amount of N1-methylinosine was detected as a result of non-enzymatic deamination of m¹A. Furthermore, the m¹A-to-m⁶A conversion was consistently observed in a biological sample. To eliminate the bias that resulted from m¹A-to-m⁶A conversion, the standard addition method was adopted. This report highlighted the challenges of having different extents of m¹A-to-m⁶A conversion under specific experimental conditions and demonstrated a viable solution for resolving the issue. Full article

(This article belongs to the Collection Feature Papers in Molecular Biomarkers)

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17 pages, 1372 KB

Open AccessArticle

Biomimetic Studies on the Reactivity of Sulfur-Centered Radicals with Purine Moieties of DNA

by Annalisa Masi, Sebastian Barata-Vallejo and Chryssostomos Chatgilialoglu

Biomolecules 2026, 16(5), 711; https://doi.org/10.3390/biom16050711 (registering DOI) - 12 May 2026

Abstract

The reaction of the HS^•/S^•− radical (pKa ~3.4), generated selectively from H₂S by γ-irradiated N₂-flushed aqueous solutions at pH 5, with purine nucleosides (dG or dA), a 10-mer double-stranded oligodeoxynucleotide (ds-ODNs), and calf thymus [...] Read more.

The reaction of the HS^•/S^•− radical (pKa ~3.4), generated selectively from H₂S by γ-irradiated N₂-flushed aqueous solutions at pH 5, with purine nucleosides (dG or dA), a 10-mer double-stranded oligodeoxynucleotide (ds-ODNs), and calf thymus (ct) DNA was investigated, under various experimental conditions. Concurrent quantification of the four purine 5′,8-cyclo-2′-deoxynucleosides (cPu) and two 8-oxo-7,8-dihydro-2′-deoxypurines (8-oxo-Pu) by LC-MS/MS analysis using isotopomeric internal standards was achieved. The formation of 8-oxo-Pu is several tens of times larger than cPu. Mechanistic schemes for the formation of the two product groups are proposed. Hydrogen atom abstraction from C5′–H by S^•− produces the cPu via cyclization of the C5′ radical onto C8, forming a new covalent bond, C5′–C8. The unexpected formation of 8-oxo-Pu should be mechanistically more complex. We propose that an S^•− (coupled with H⁺) adds to the base rings, followed by the elimination of HS⁻ to form the corresponding radical cation; subsequent reactions with H₂O and radical disproportionation with another S^•− lead to 8-oxo-Pu. A comparison of S^•− with the available literature data for HO^• reactivity towards ct-DNA in de-oxygenated aqueous solutions is also presented. Before the present findings, cPu lesions were attributed exclusively to HO^• reactivity toward ct-DNA. The reaction of the thiyl radical (HOCH₂CH₂S^•) with ct-DNA was also investigated, yielding results similar to those of S^•− obtained under comparable experimental conditions. Our results contributed to a better understanding of DNA damage induced by reactive sulfur species (RSS), particularly the formation of purine lesions and the relative abundance of cPu versus 8-oxo-Pu. Full article

(This article belongs to the Section Molecular Biomarkers)

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22 pages, 975 KB

Open AccessReview

Microenvironmental Drivers of Bone Disease in Multiple Myeloma: Oxidative Stress, Sterile Inflammation, Autophagy–Lysosomal Remodeling, and the Iron–Lipid Peroxidation Axis

by Maria Elisa Nasso, Adele Bottaro, Manlio Fazio, Fabio Stagno, Sebastiano Gangemi and Alessandro Allegra

Biomolecules 2026, 16(5), 710; https://doi.org/10.3390/biom16050710 (registering DOI) - 12 May 2026

Abstract

Multiple myeloma profoundly remodels the bone marrow microenvironment, causing osteolytic bone disease through a persistent uncoupling of bone resorption and formation. Beyond the canonical roles of the receptor activator of nuclear factor kappa-B ligand/receptor activator of nuclear factor kappa-B/osteoprotegerin triad and Wnt antagonism, [...] Read more.

Multiple myeloma profoundly remodels the bone marrow microenvironment, causing osteolytic bone disease through a persistent uncoupling of bone resorption and formation. Beyond the canonical roles of the receptor activator of nuclear factor kappa-B ligand/receptor activator of nuclear factor kappa-B/osteoprotegerin triad and Wnt antagonism, three interdependent stress programs orchestrate the osteolytic niche. These include oxidative stress driven by mitochondrial and nicotinamide adenine dinucleotide phosphate oxidase-derived reactive oxygen species; sterile inflammation sustained by damage-associated molecular patterns, pattern-recognition receptors, and pro-inflammatory cytokines; and autophagy–lysosomal remodeling governed by transcription factor EB and the coordinated lysosomal expression and regulation network. These axes intersect with iron handling and lipid peroxidation to regulate sensitivity to ferroptotic cell death, thereby shaping osteoclast priming, osteoblast suppression, and matrix turnover. Building on these mechanistic insights, we outline a translational framework that aligns standardized bone turnover markers of formation and resorption with composite panels of oxidative and nitrosative stress. This framework also integrates modern imaging to capture structural injury and metabolically active marrow disease. We further propose a therapeutic roadmap layered on antiresorptive foundations that targets selective inhibition of nicotinamide adenine dinucleotide phosphate oxidase 4 and calibrated modulation of nuclear factor erythroid 2–related factor 2, disrupts damage-associated molecular pattern and cytokine circuits, and applies lineage- and timing-specific tuning of autophagy together with restoration of ferroportin-1 or iron chelation. This integrated strategy is designed to recouple bone remodeling and improve clinically meaningful skeletal outcomes in multiple myeloma. Full article

(This article belongs to the Special Issue Molecular Factors Involved in Healthy and Diseased States of Skeletal Muscle: Overview and Perspectives)

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33 pages, 4547 KB

Open AccessReview

Mechanism and Therapeutic Potential of Viral Mimicry in Cancer Immunotherapy

by Alisha Pearl Kirkland, Mahek Shah and Charles Spruck

Biomolecules 2026, 16(5), 709; https://doi.org/10.3390/biom16050709 (registering DOI) - 12 May 2026

Abstract

Cancer immunotherapy has transformed oncology by harnessing the immune system to recognize and eliminate malignant cells. However, many cancers exhibit limited or variable responses to this class of treatment due to insufficient antigen presentation and impaired interferon (IFN) signaling, creating an immunologically “cold” [...] Read more.

Cancer immunotherapy has transformed oncology by harnessing the immune system to recognize and eliminate malignant cells. However, many cancers exhibit limited or variable responses to this class of treatment due to insufficient antigen presentation and impaired interferon (IFN) signaling, creating an immunologically “cold” tumor microenvironment (TME) characterized by poor immune cell infiltration and treatment resistance. Viral mimicry has emerged as a therapeutic strategy to overcome these limitations by reactivating innate antiviral pathways within tumor cells. Viral mimicry occurs through the reactivation of endogenous retroviruses (ERVs) and other retrotransposons (e.g., LINE-1), which subsequently stimulate downstream nucleic acid sensing pathways. The resulting type I/III IFN responses restore antigen presentation and attract cytotoxic immune cells, sensitizing resistant tumors to immunotherapy. However, systemic stimulation of these pathways can trigger context-dependent inflammation and adaptive resistance, highlighting the need for temporal and spatial control. In this review, we examine the mechanistic foundation and clinical trajectory of viral mimicry, with an emphasis on its potential integration with established treatments and engineered immune cell platforms. By identifying the molecular and clinical gaps, viral mimicry can be harnessed to enhance tumor-specific immune activation and overcome treatment resistance in cancer immunotherapy. Full article

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39 pages, 7398 KB

Open AccessArticle

Gut-Derived Lipid Mediators Orchestrate Ovarian Metabolic Homeostasis and Clutch Persistence in Aging Laying Hens via the PLA2G6-ALOX15B-AGPAT3 Axis

by Xin Li, Xiaoliang Wang, Xia Cai, Qiang Meng, Yanyan Sun, Changsuo Yang and Junfeng Yao

Biomolecules 2026, 16(5), 708; https://doi.org/10.3390/biom16050708 (registering DOI) - 11 May 2026

Abstract

Clutch persistence, defined as the ability to sustain consecutive egg-laying cycles, is a pivotal determinant of profitability in the poultry industry, particularly for aging laying hens (≥65 weeks). However, the molecular mechanisms governing this trait remain elusive, largely due to the traditional “ovary-centric” [...] Read more.

Clutch persistence, defined as the ability to sustain consecutive egg-laying cycles, is a pivotal determinant of profitability in the poultry industry, particularly for aging laying hens (≥65 weeks). However, the molecular mechanisms governing this trait remain elusive, largely due to the traditional “ovary-centric” paradigm that overlooks systemic regulation by the gut microbiota. To address this knowledge gap, the present study aimed to dissect the comprehensive regulatory network governing clutch persistence using integrated multi-omics analyses. A total of 20 sixty-five-week-old Rhode Island Red (RIR) laying hens with cumulative egg production exceeding 300 eggs but distinct clutch persistence were stratified into a high-clutch persistence group (HCP, ≥25 clutches, n = 10) and a low-clutch persistence group (LCPLCP, ≤15 clutches, n = 10). Multi-omics profiling, including ovarian transcriptomics, proteomics, and metabolomics; serum metabolomics; and cecal microbiota 16S rRNA sequencing was performed. Data integration and association mining were conducted via Spearman correlation analysis with stringent thresholds (r > 0.6, p < 0.01). Integrated analyses revealed a “gut–ovary axis” regulatory model mediated by a lipid mediator network, operating through a three-tiered mechanism: (1) Gut Initiation: The HCP group exhibited enriched cecal γ-Proteobacteria, which promoted biosynthesis of lipid precursors. (2) Serum Transport: Key serum lipid mediators, most notably LysoPC (22:6) (VIP = 4.5) and cholesterol ester CE (20:4), served as critical carriers transducing gut-derived signals to the ovary. (3) Ovarian Execution: These lipid signals activated a core ovarian metabolic pathway centered on the PLA2G6-ALOX15B-AGPAT3 axis, which coordinated follicular development and ovulation by supplying steroid hormone synthesis substrates, exerting anti-inflammatory effects, and stabilizing membrane structures. Collectively, this study demonstrates that gut microbiota modulates clutch persistence in aging laying hens via lipid mediators, orchestrating a systemic “gut–serum–ovary” regulatory cascade. These findings provide a novel molecular framework for extending the economic egg-laying cycle through the targeted manipulation of intestinal microbiota or serum lipid metabolism. Full article

(This article belongs to the Section Lipids)

16 pages, 1998 KB

Open AccessArticle

GPIHBP1 as a Biomarker of Diabetic Polyneuropathy and Vascular Complications in Type 2 Diabetes Mellitus

by Savelia Yordanova, Antoaneta Gateva, Diana Nikolova, Julieta Hristova and Zdravko Kamenov

Biomolecules 2026, 16(5), 707; https://doi.org/10.3390/biom16050707 (registering DOI) - 11 May 2026

Abstract

Background: Diabetic neuropathy is one of the most common chronic complications of diabetes mellitus and could lead to foot ulcerations, lower-limb amputations, increased mortality and reduced quality of life. This study examines the level of GPIHBP1 to assess its diagnostic and prognostic values [...] Read more.

Background: Diabetic neuropathy is one of the most common chronic complications of diabetes mellitus and could lead to foot ulcerations, lower-limb amputations, increased mortality and reduced quality of life. This study examines the level of GPIHBP1 to assess its diagnostic and prognostic values across the metabolic continuum. Methods: This is an observational monocentric study, including 160 patients with type 2 diabetes mellitus, obesity without carbohydrate metabolism disorders and healthy controls. Clinical data and laboratory results were collected, and serum levels of GPIHBP1 were measured using an ELISA. The presence of DPN for the diabetes group was assessed using corneal confocal microscopy and NDS. The statistical analyses included t-tests, Pearson’s correlation analysis, and ROC analysis to explore associations and the predictive values of the biomarker. Results: The GPIHBP1 levels increased progressively, with the lowest levels observed in the control group, higher levels in patients with obesity, and the highest levels in those with diabetes mellitus. Higher GPIHBP1 levels were observed in patients with peripheral diabetic neuropathy compared to those without. GPIHBP1 demonstrated moderate discriminative performance for the presence of diabetes, diabetic neuropathy and nephropathy. GPIHBP1 levels were also associated with renal function parameters and markers of vascular involvement. After adjustment for confounders, including estimated glomerular filtration rate (eGFR), the association between GPIHBP1 and diabetic neuropathy remained statistically significant although attenuated. Higher levels were observed in patients with coronary artery disease, and a positive correlation was established with mean IMT and sudomotor dysfunction score. Conclusions: Circulating GPIHBP1 levels are associated with diabetes mellitus and its micro- and macrovascular complications, particularly diabetic neuropathy. Its measurement could enhance early diagnosis and personalized management of T2DM, and, while these findings support a potential role of GPIHBP1 as a biomarker of metabolic and vascular dysfunction, its clinical utility requires confirmation in longitudinal studies. Full article

(This article belongs to the Section Molecular Biomarkers)

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13 pages, 8499 KB

Open AccessArticle

Immunohistochemical Evaluation of Integrin β6 Expression in Triple-Negative Breast Cancer as a Predictive Biomarker for Therapeutic and Diagnostic Radionuclides

by Muin Tuffaha, Wael Hananeh, Nikola Bangemann, Amro Tuffaha and Michael Starke

Biomolecules 2026, 16(5), 706; https://doi.org/10.3390/biom16050706 (registering DOI) - 11 May 2026

Abstract

Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype associated with limited therapeutic options and poor clinical outcomes. The aim of this research is to assess the prevalence, intensity, and distribution of integrin αvβ6 expression in TNBC using immunohistochemistry and to evaluate [...] Read more.

Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype associated with limited therapeutic options and poor clinical outcomes. The aim of this research is to assess the prevalence, intensity, and distribution of integrin αvβ6 expression in TNBC using immunohistochemistry and to evaluate its potential as a predictive biomarker for αvβ6-targeted radionuclide therapy and other αvβ6-targeted theranostic approaches. Immunohistochemical analysis of integrin αvβ6 was performed on formalin-fixed, paraffin- embedded tumor samples from 48 patients with histologically confirmed TNBC. Staining intensity and the proportion of positive tumor cells were assessed using a semi-quantitative scoring system, and expression patterns were analyzed with regard to cellular localization and intratumoral heterogeneity. Moderate to strong integrin αvβ6 expression was observed in 43.8% of cases, with strong expression (≥50% of tumor cells) present in 25%. Expression was predominantly membranous, with occasional cytoplasmic staining, and demonstrated marked inter- and intratumoral heterogeneity. Integrin αvβ6 is frequently expressed in TNBC and represents a promising biomarker for patient selection in αvβ6-targeted radionuclide imaging and therapy. These findings provide a strong biological rationale for the clinical translation of integrin-targeted radioligands and support the development of personalized radiotheranostic strategies in TNBC. Full article

(This article belongs to the Section Molecular Medicine)

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72 pages, 2076 KB

Open AccessReview

Plant-Derived Nanovesicles: A Comprehensive Review from Isolation to Clinical Translation—Unlocking Natural Nanocarriers for Biomedical Applications

by Xinyan Wang, Chenchen Yuan and Rong Lu

Biomolecules 2026, 16(5), 705; https://doi.org/10.3390/biom16050705 (registering DOI) - 11 May 2026

Abstract

Plant-derived nanovesicles (PDNVs) are a class of nanoscale vesicles derived from plant tissues; they are particles with a lipid bilayer and no ability to replicate autonomously. As a type of bioactive natural nanocarrier, they demonstrate immense potential for application in 21st-century nanomedicine, skincare [...] Read more.

Plant-derived nanovesicles (PDNVs) are a class of nanoscale vesicles derived from plant tissues; they are particles with a lipid bilayer and no ability to replicate autonomously. As a type of bioactive natural nanocarrier, they demonstrate immense potential for application in 21st-century nanomedicine, skincare and nutritional health, owing to their excellent biocompatibility, low immunogenicity and targeted delivery capabilities. However, the clinical translation of PDNVs still faces key bottlenecks, including low extraction efficiency, complex purification processes, and immature engineering modification techniques. Compared to the wealth of systematic reviews in the field of Mammalian Extracellular Vesicles (M-EVs), research on PDNVs still lacks a comprehensive exposition of its multifaceted research progress. This review endeavours to comprehensively summarise the shortcomings over the last 60 years regarding PDNV purification processes, research progress, composition and characterisation, engineering modifications, functional mechanisms, clinical translation and market regulation. It discusses the feasibility of innovative approaches such as AI deep learning technologies, interdisciplinary integration and cross-application, and outlines the latest frontiers in PDNV research. It provides comprehensive and reliable reference material for future research and application strategies regarding PDNVs, offering theoretical support and practical guidance to overcome barriers to their industrialisation. This will facilitate the transition from limited laboratory research to clinical application and drive technological innovation in the next generation of naturally derived nanomedicines. Full article

(This article belongs to the Section Natural and Bio-derived Molecules)

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23 pages, 1343 KB

Open AccessArticle

Exploring Replicative Senescence and Oxidative Stress-Induced Remodelling of Mitochondrial-Associated Membranes in Human Skin Fibroblasts

by Anne-Laure Bulteau, Gallic Beauchef, Stéphanie Chanon, Aurélie Vieille-Marchis, Julien Chlasta, Gaël Runel, Juliette Sage, Tanesha Naiken, Lauren Sobilo, Elodie Bossard, Lorene Gourguillon, Carine Nizard, Karl Pays, Laurence Canaple and Beatrice Morio

Biomolecules 2026, 16(5), 704; https://doi.org/10.3390/biom16050704 (registering DOI) - 11 May 2026

Abstract

(1) Background: Calcium transfer between the endoplasmic reticulum (ER) and mitochondria through the IP3R–VDAC1 complex at mitochondria-associated ER membranes (MAMs) is essential for cellular homeostasis. Alterations in this signalling axis have been implicated in ageing and cellular senescence. (2) Methods: We developed an [...] Read more.

(1) Background: Calcium transfer between the endoplasmic reticulum (ER) and mitochondria through the IP3R–VDAC1 complex at mitochondria-associated ER membranes (MAMs) is essential for cellular homeostasis. Alterations in this signalling axis have been implicated in ageing and cellular senescence. (2) Methods: We developed an in vitro human dermal fibroblast (HDF) model combining replicative senescence and acute oxidative stress to investigate the role of ER–mitochondria coupling in skin ageing and to enable biomolecule screening. (3) Results: In situ proximity ligation assays revealed that replicative senescence significantly increased the number of VDAC1/IP3R complexes per cell (+85% and +72%, p < 0.01), together with elevated cellular reactive oxygen species (+47% and +74%, p < 0.05). Consistently, acute oxidative stress (50 µM t-BHP, 30 min) rapidly increased VDAC1/IP3R complexes (+48%, p < 0.001) and intra-mitochondrial calcium levels (+19%, p < 0.001). These effects persisted for 24 h post-treatment and were associated with impaired mitochondrial function (−27% in the Bioenergetic Health Index, p < 0.05). We also established a flexibility index capturing both acute and long-term adaptations and detecting the protective effects of an orchid extract. (4) Conclusions: ER–mitochondria coupling disruption via the IP3R–VDAC1 complex may contribute to oxidative stress-induced senescence and represent a key mechanism in extrinsic skin ageing. Full article

(This article belongs to the Special Issue Mitochondrial ROS in Health and Disease: 2nd Edition)

18 pages, 3602 KB

Open AccessArticle

A Liposomal Delivery System of Blueberry Anthocyanins Ameliorates Corneal Laser Injury

by Zihan Lv, Chaoran Li, Di Liang, Guangrui Chen, Mengqi Qiu, Zhiyun Meng, Ruolan Gu, Hui Gan, Zhuona Wu, Zaifu Yang and Guifang Dou

Biomolecules 2026, 16(5), 703; https://doi.org/10.3390/biom16050703 (registering DOI) - 11 May 2026

Abstract

This study aims to develop and systematically evaluate a new lipid-based formulation of blueberry anthocyanins, which can accelerate the healing effect of the cornea. The study first successfully screened and optimized the formulation and preparation process for blueberry anthocyanin liposomes. Characterization via transmission [...] Read more.

This study aims to develop and systematically evaluate a new lipid-based formulation of blueberry anthocyanins, which can accelerate the healing effect of the cornea. The study first successfully screened and optimized the formulation and preparation process for blueberry anthocyanin liposomes. Characterization via transmission electron microscopy and dynamic light scattering revealed uniformly distributed, near-spherical liposomes with distinct phospholipid bilayers. Key physicochemical parameters—particle size, zeta potential, encapsulation efficiency, and drug loading capacity—all met formulation standards. In vivo pharmacodynamic experiments demonstrated that topical administration of blueberry anthocyanin liposomes significantly accelerated the repair process and effectively mitigated depressional damage to the corneal epithelium in a New Zealand white rabbit corneal injury model induced by 10.6 μm mid-infrared CO₂ laser. In summary, the blueberry anthocyanin liposomes successfully prepared in this study exhibit excellent performance, effectively enhancing drug exposure levels in vivo and promoting corneal repair. This provides reliable experimental evidence for the development of plant natural active ingredients in ophthalmic treatments. Full article

(This article belongs to the Special Issue Feature Papers in the Natural and Bio-Derived Molecules Section)

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11 pages, 1288 KB

Open AccessCommunication

Plasma Expression and In Silico Functional Analysis of miR-106b-5p and miR-185-5p in Chronic Heart Failure

by Phuong Anh Huynh, Bao-Quoc Vu, Vu Hoang Vu, Minh Hoang and Diem My Vu

Biomolecules 2026, 16(5), 702; https://doi.org/10.3390/biom16050702 (registering DOI) - 11 May 2026

Abstract

Heart failure (HF) is one of the largest contributors to disease burden and healthcare expenditure worldwide. Countless studies have shown that microRNAs (miRNAs) are pivotal regulators of heart homeostasis and promising biomarkers for the diagnosis and management of HF. Among the reported miRNAs, [...] Read more.

Heart failure (HF) is one of the largest contributors to disease burden and healthcare expenditure worldwide. Countless studies have shown that microRNAs (miRNAs) are pivotal regulators of heart homeostasis and promising biomarkers for the diagnosis and management of HF. Among the reported miRNAs, miR-106b-5p and miR-185-5p have been implicated in various cardiovascular diseases through involvement in cardiac injury, fibrosis, and cell survival pathways. Although cellular functions of miR-106b-5p and miR-185-5p have been investigated intensively, their circulating levels remain largely elusive in patients with HF. This study examined expression levels of plasma miR-106b-5p and miR-185-5p by quantitative reverse transcription PCR (RT-qPCR) in a study cohort comprising 41 chronic HF patients and 41 matched, non-HF subjects. Bioinformatic analysis was conducted for miR-106b-5p and miR-185-5p to discover their potential target genes, biological functions, and association with cardiovascular-related clinical phenotypes. Chronic HF patients presented a significant increase in plasma miR-106b-5p and miR-185-5p levels. Diverse expressive patterns of miR-106b-5p and miR-185-5p were observed in different types and functional classes of HF. A positive correlation between plasma miR-106b-5p and miR-185-5p was also identified. In silico analysis suggested that many genes related to cell proliferation and metabolic pathways were shared targets of miR-106b-5p and miR-185-5p. Our study reveals dysregulation of plasma miR-106b-5p and miR-185-5p in patients with chronic HF that may contribute to the pathological course of this disease. Full article

(This article belongs to the Special Issue The Role of Non-Coding RNAs in Health and Disease: 2nd Edition)

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16 pages, 1419 KB

Open AccessReview

Rewiring Adipocyte Plasticity: The Redox–Mitochondrial Axis as a Driver of Beige Fat Immunometabolism and Adipose Inflammation

by Faycal Aissa-Brahim, Shuwen Yang, Xunyong Zhou, Zhong Li and Su Bu

Biomolecules 2026, 16(5), 701; https://doi.org/10.3390/biom16050701 (registering DOI) - 9 May 2026

Abstract

Obesity is a major health crisis that impacts social and economic burdens worldwide, and it is being studied intensively to understand the molecular mechanisms and regulators of this complex condition. Over the past decade, significant insights into adipocyte fate have been gained, demonstrating [...] Read more.

Obesity is a major health crisis that impacts social and economic burdens worldwide, and it is being studied intensively to understand the molecular mechanisms and regulators of this complex condition. Over the past decade, significant insights into adipocyte fate have been gained, demonstrating that adipocyte behavior is influenced by intracellular pathways, systemic mediators, and environmental signals. In this review, we discuss the current understanding of key molecular and functional changes in adipose tissue. We focused on ER–mitochondrial dynamics and their role in beige adipocytes. We examined the biological properties of beige fat cells, including their inflammatory status, redox balance, and regulation of adipocyte transdifferentiation via signaling molecules. Finally, we explored the effects of naturally derived compounds on adipocyte function and their potential to combat obesity using a comprehensive approach. The process of adipocyte beiging induced by coordinated intracellular signaling pathways highlights mechanisms that can reprogram metabolic homeostasis and reduce obesity-related phenotypes. Full article

(This article belongs to the Section Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates)

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17 pages, 3890 KB

Open AccessArticle

In Silico and In Vitro Evaluation of Bioactive Constituents Isolated from Ziziphus oxyphylla for the Treatment of Diabetes

by Muhammad Zia-Ul-Haq, Waqar Ahmad Kaleem, Syeda Ayesha Farhana, Syed Uzair Ali Shah, Abdul Rehman, Saqib Khan and Iffat Naz

Biomolecules 2026, 16(5), 700; https://doi.org/10.3390/biom16050700 (registering DOI) - 9 May 2026

Abstract

Zizyphus oxyphylla has been traditionally used in the management of metabolic disorders, and cyclopeptide alkaloids isolated from its roots have been structurally characterized, although their antidiabetic potential remains insufficiently explored. This study evaluated the antidiabetic activity of three previously isolated cyclopeptide alkaloids, Oxyphylline-D [...] Read more.

Zizyphus oxyphylla has been traditionally used in the management of metabolic disorders, and cyclopeptide alkaloids isolated from its roots have been structurally characterized, although their antidiabetic potential remains insufficiently explored. This study evaluated the antidiabetic activity of three previously isolated cyclopeptide alkaloids, Oxyphylline-D (1), Nummularine-C (2), and Nummularine-R (3), using integrated in silico molecular docking and in vitro enzyme inhibition assays. Molecular docking was performed against key diabetes-related enzymes, including α-amylase, α-glucosidase, and dipeptidyl peptidase-4, followed by validation through enzyme inhibition assays. All compounds demonstrated favorable binding affinities toward the selected targets, with compound 2 showing the most consistent performance across enzymes. In vitro results support these findings, where compound 2 exhibited inhibitory activity with IC₅₀ values of 102.97 µg/mL (187.71 µM) against α-amylase and 28.87 µg/mL (52.62 µM) against dipeptidyl peptidase-4, comparable to standard inhibitors. Overall, the results indicate that cyclopeptide alkaloids from Z. oxyphylla possess significant multi-target antidiabetic potential, with Nummularine-C emerging as a promising candidate for further pharmacological development. These findings provide experimental support for computational predictions and reinforce the relevance of combining in silico and in vitro approaches for identifying bioactive natural products with potential therapeutic value in diabetes management, drug discovery pipelines, and development. Full article

(This article belongs to the Section Natural and Bio-derived Molecules)

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14 pages, 2095 KB

Open AccessReview

A Narrative Review of Recent Insights on Nerve Growth Factor Signaling in Physiological and Pathological Ovarian Processes in Mammals

by Massimo Aloisi, Gianna Rossi and Sandra Cecconi

Biomolecules 2026, 16(5), 699; https://doi.org/10.3390/biom16050699 - 8 May 2026

Abstract

Nerve Growth Factor (NGF), a member of the neurotrophin family, is currently regarded as a key regulator of ovarian physiology beyond its well-known neurotrophic functions. The mammalian ovary is one of the most highly innervated peripheral organs. Increasing evidence indicates that NGF and [...] Read more.

Nerve Growth Factor (NGF), a member of the neurotrophin family, is currently regarded as a key regulator of ovarian physiology beyond its well-known neurotrophic functions. The mammalian ovary is one of the most highly innervated peripheral organs. Increasing evidence indicates that NGF and its receptors, TrkA and p75NTR, are widely expressed in ovarian tissues. Through the activation of the PI3K/AKT, MAPK/ERK, and PLCγ signaling pathways, NGF influences granulosa cell proliferation, steroidogenesis, and ovulation. Physiological levels of NGF are essential for primordial follicle activation, FSH receptor expression, and effective bidirectional communication between oocytes and surrounding somatic cells. As a result, NGF also regulates oocyte maturation and developmental competence. The disruption of NGF signaling can lead to serious health issues. Both low and high levels of NGF negatively affect folliculogenesis and fertility. Elevated intraovarian NGF results in sympathetic over-innervation, altered steroid production, and polycystic ovarian features. In addition, increased NGF expression has been linked to endometriosis and ovarian cancer progression. Clinical studies further suggest that follicular NGF levels may serve as indicators of ovarian reserve and reproductive outcomes in assisted reproduction. This narrative review synthesizes the current knowledge on NGF roles in ovarian physiology and disease. It highlights NGF’ dual functions as a central regulator of follicular dynamics, and as a potential biomarker and therapeutic target for common reproductive system diseases. Full article

(This article belongs to the Collection Feature Papers in Molecular Reproduction)

14 pages, 716 KB

Open AccessArticle

Clinical Relevance and Methodological Comparison of Anti-MDA5 Antibody Detection: A Five-Year Retrospective and Exploratory Pilot Study

by Sándor Mogyoróssy, Gábor Nagy, Zoltán Griger, Melinda Nagy-Vincze, Monika Bodoki, Dóra Csige, Tünde Tarr, Éva Zöld, György Pfliegler, Boglárka Csilla Brúgós, Hui Lu, Sarah Tansley, Péter Antal-Szalmás, Andrea Domján, Szilvia Szamosi, Gabriella Szűcs, Zoltán Szekanecz, Ágnes Horváth and Levente Bodoki

Biomolecules 2026, 16(5), 698; https://doi.org/10.3390/biom16050698 - 8 May 2026

Abstract

Anti-melanoma differentiation-associated gene 5 (anti-MDA5) antibodies are critical biomarkers in myositis, associated with distinct clinical features and prognosis. This study aimed to evaluate the proportion of anti-MDA5 positivity and compare the diagnostic performance of local immunoblotting (IB) with gold-standard immunoprecipitation (IP). We performed [...] Read more.

Anti-melanoma differentiation-associated gene 5 (anti-MDA5) antibodies are critical biomarkers in myositis, associated with distinct clinical features and prognosis. This study aimed to evaluate the proportion of anti-MDA5 positivity and compare the diagnostic performance of local immunoblotting (IB) with gold-standard immunoprecipitation (IP). We performed a retrospective analysis of 3272 physician-requested anti-MDA5 IB determinations over a five-year period (2019–2023). A subsequent exploratory pilot study of ten Hungarian patients with myositis was conducted to compare IB results with radiolabeled protein IP. Confirmatory in-house enzyme-linked immunosorbent assay (ELISA) was used to distinguish between 140 kDa bands (anti-MDA5 vs. anti-NXP2). Indirect immunofluorescence (IIF) on HEp-2 cells was also evaluated. In the retrospective cohort, 3.7% (n = 121) of samples were non-negative. Among 64 borderline patients, only one (1.6%) had a definitive diagnosis of dermatomyositis (DM). Conversely, the proportion of confirmed myositis cases was notably higher among patients with strong positive IB results. In our exploratory cross-sectional pilot study, complete concordance between the two assays was observed for negative and strong positive results. Discrepancies were noted in borderline and weak positivity ranges, where anti-MDA5 was not detected by IP; instead, alternative autoantibodies were identified. The three IP-confirmed MDA5 positive samples were all validated by ELISA. The characteristic IIF cytoplasmic staining was identifiable in 2 out of 10 cases (20%). In our cohort, borderline IB cases were frequently potential false positives, highlighting the need for careful clinical evaluation. Borderline and weak results require clinical correlation or confirmatory testing to avoid misdiagnosis. Full article

(This article belongs to the Section Molecular Medicine)

17 pages, 899 KB

Open AccessArticle

Effects of Loop Nucleobase Substitution on G-Quadruplex Thermal Stability in Aqueous Glycine Betaine, Proline, TMAO, and Urea Solutions

by Jeffrey J. Schwinefus, Marija Corluka, Isabella Dobrinski, Stella L. Jaeckle, Joshua Kim, Grace Knowlan, Hannah Omodt, Noah Otto, Mari V. Reid, Reid Rognerud and Kathryn M. Stein

Biomolecules 2026, 16(5), 697; https://doi.org/10.3390/biom16050697 - 8 May 2026

Abstract

G-quadruplexes are guanine-rich DNA or RNA structures comprising two or more stacked guanine tetrads (G-quartet) with nucleobases in the loops linking the G-quartets. The thermal stability of the thrombin-binding aptamer G2 d(G₂T₂G₂TGTG₂T₂G₂ [...] Read more.

G-quadruplexes are guanine-rich DNA or RNA structures comprising two or more stacked guanine tetrads (G-quartet) with nucleobases in the loops linking the G-quartets. The thermal stability of the thrombin-binding aptamer G2 d(G₂T₂G₂TGTG₂T₂G₂) G-quadruplex was quantified using m-values in aqueous glycine betaine (GB), proline, TMAO, and urea solutions using UV-absorbance spectroscopy. The thermal stability of the G2 variants was also explored with nucleobase substitutions in the TGT loop (TAT, TCT, TTT, UGU, and UUU), in the T₂ loops (T₄, U₂), or in both loops (UGU and U₂, UUU and U₂). GB and TMAO strongly stabilized G2 and its variants. Urea weakly destabilized G2 and its variants, while proline acted as a weak stabilizer or destabilizer depending on G2 variant nucleobase sequence. Both the unfolding enthalpy and entropy were positively correlated with cosolute molality for all cosolute and G-quadruplex combinations. Analysis of the change in solvent-accessible surface area (ΔASA) after unfolding G2 suggested the stability of G2 and its variants in aqueous cosolute solutions was driven by favorable interaction of cosolutes with G-quartet ΔASA and net-favorable or unfavorable interactions with the loop ΔASA. Our results reinforce a general mechanism of folded DNA and RNA stability modulation in cosolute solutions. Full article

(This article belongs to the Section Molecular Biophysics: Structure, Dynamics, and Function)

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16 pages, 2583 KB

Open AccessArticle

Functional Aspects of Fibrin Structure Alterations by Tranexamic Acid in the Inhibition of Fibrinolysis

by Kata Balog Virag, Barbara Baráth, Kristóf Molnár, Petra Csikós, Alexandra Raska, László Szabó, Natalia Nikolova, Kiril Tenekedjiev, Krasimir Kolev and Nikolett Wohner

Biomolecules 2026, 16(5), 696; https://doi.org/10.3390/biom16050696 - 8 May 2026

Abstract

Background: Tranexamic acid (TXA) is a synthetic lysine analog widely used as an antifibrinolytic agent. Large randomized trials have demonstrated life-saving benefits when TXA is administered early in acute hemorrhage, but results regarding prophylactic administration have been conflicting, and several trials have not [...] Read more.

Background: Tranexamic acid (TXA) is a synthetic lysine analog widely used as an antifibrinolytic agent. Large randomized trials have demonstrated life-saving benefits when TXA is administered early in acute hemorrhage, but results regarding prophylactic administration have been conflicting, and several trials have not shown improved clinical outcomes. The mechanisms underlying this discrepancy remain incompletely understood. Objectives: To investigate the molecular and structural mechanisms that determine TXA efficacy in purified fibrin clots under conditions mimicking therapeutic versus prophylactic administration. Methods: We examined fibrinolysis induced by tissue plasminogen activator (tPA) in vitro using confocal microscopy, viscoelastic testing (ClotPro), turbidimetry, and plasmin generation assays at physiologically and therapeutically relevant concentrations of plasminogen and TXA. Scanning electron microscopy (SEM) was employed to assess fibrin structure. Results: When TXA was incorporated into fibrin clots before the addition of tPA, physiological plasminogen concentrations (2.5 µM) reversed the antifibrinolytic effect, resulting in paradoxical acceleration of lysis. By contrast, when clotting and fibrinolysis occurred simultaneously in the presence of TXA and tPA, TXA consistently prolonged lysis time irrespective of plasminogen concentration. SEM demonstrated that TXA, even at concentrations as low as 16 µM, doubled the top-quartile values of the fibrin fiber diameter, altering susceptibility to plasmin-mediated degradation without accelerating plasminogen activation. Conclusions: TXA efficacy is determined not only by dose but also by timing and the plasminogen availability in the clot microenvironment. These findings provide mechanistic insight into the failure of prophylactic TXA administration and highlight the importance of context in optimizing its clinical use. Full article

(This article belongs to the Special Issue Fibrinogen and Fibrin in Human Diseases)

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20 pages, 1708 KB

Open AccessArticle

From Metabolomics to Function: Ranking Plant Stem Cell Metabolomes for Use in Health and Cosmetics

by Assaf Zemach, Mikhail R. Plaza, Bong Seop Lee, Leo Little Dog, Efrain Santiago-Rodriguez, Dior Simmons, Melissa Palomares, Dodanim Talavera-Adame and Nathan Newman

Biomolecules 2026, 16(5), 695; https://doi.org/10.3390/biom16050695 - 7 May 2026

Abstract

Plants produce diverse metabolites with potential benefits for human health. However, the metabolomes of plant callus cultures—cell cultures analogous to stem cells—remain poorly characterized in terms of their functional relevance. This study aimed to systematically profile and functionally annotate metabolites from diverse plant [...] Read more.

Plants produce diverse metabolites with potential benefits for human health. However, the metabolomes of plant callus cultures—cell cultures analogous to stem cells—remain poorly characterized in terms of their functional relevance. This study aimed to systematically profile and functionally annotate metabolites from diverse plant callus cultures to better understand their potential biological activities and applications. We profiled the metabolomes of six plant calli: Acacia concinna (Shikakai), Daucus carota (carrot), Hibiscus sabdariffa (hibiscus), Linum usitatissimum (flax), Ocimum sanctum (tulsi), and the Nicotiana tabacum Bright-Yellow 2 (BY-2) cell line. To facilitate functional interpretation, we developed Metabolite2Function (M2F), a pipeline that annotates metabolites with biological functions using scientific literature and large language modeling. Untargeted metabolomics identified 177 metabolites, revealing clustering patterns independent of genetic relationships, culture age, or growth rate. Tulsi and carrot calli exhibited enrichment in metabolites relative to the tobacco reference line, whereas flax and hibiscus were comparatively depleted. Most metabolites varied across at least four calli, and 10% were unique to a single species. Using M2F, we annotated 87 metabolites with beneficial activities, including antioxidant, anti-glycation, anti-inflammatory, and anti-senescence functions, as well as skin-related effects such as collagen production and brightening. Notably, antioxidant and anti-senescence metabolite levels correlated with corresponding biological activities in human cells. Plant callus cultures generate distinct and functionally diverse bioactive metabolomes. M2F provides a scalable framework for systematic functional annotation relevant to human health and cosmetic applications. Full article

(This article belongs to the Section Bioinformatics and Systems Biology)

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15 pages, 1413 KB

Open AccessReview

Mcl1 as a Molecular Switch Linking Inflammatory Bowel Diseases to Colorectal Tumorigenesis

by Ahmed M. Elshazly, Jiong Li, Guang-Yu Yang and Senthil K. Radhakrishnan

Biomolecules 2026, 16(5), 694; https://doi.org/10.3390/biom16050694 - 7 May 2026

Abstract

The maintenance of gastrointestinal homeostasis relies on a tightly coordinated interplay between the intestinal epithelium, the immune system, and the commensal microbiome. Disruption of this balance underlies inflammatory bowel disease (IBD), encompassing Crohn’s disease and ulcerative colitis, and is characterized by chronic, relapsing [...] Read more.

The maintenance of gastrointestinal homeostasis relies on a tightly coordinated interplay between the intestinal epithelium, the immune system, and the commensal microbiome. Disruption of this balance underlies inflammatory bowel disease (IBD), encompassing Crohn’s disease and ulcerative colitis, and is characterized by chronic, relapsing mucosal inflammation driven by genetic susceptibility, environmental factors, immune dysregulation, and microbial imbalance. Persistent inflammation promotes repeated cycles of epithelial injury and aberrant repair, creating a permissive environment for dysplasia and the development of colitis-associated cancer, most notably colorectal carcinoma. Recent evidence identifies the anti-apoptotic regulator myeloid cell leukemia-1 (Mcl1) as a critical determinant of epithelial integrity and cellular turnover during mucosal stress. Loss or destabilization of Mcl1 disrupts epithelial homeostasis, amplifies inflammatory signaling, and accelerates tumor initiation, whereas its adaptive upregulation in established malignancy promotes tumor cell survival, metabolic fitness, and therapeutic resistance. Thus, Mcl1 functions as a context-dependent molecular switch via restraining malignant transformation during chronic inflammation while supporting tumor progression once neoplasia is established. This functional duality positions Mcl1 as both a biomarker of disease progression and a therapeutically actionable vulnerability. In this review, we synthesize recent advances elucidating how Mcl1 integrates epithelial cell-fate decisions, immune signaling and tumor evolution across the IBD–cancer continuum. We further support these concepts through integrative analyses of multiple transcriptomic datasets comparing normal colonic mucosa with colorectal tumors, and we discuss emerging pharmacological strategies targeting Mcl1 in colitis-associated cancer. Full article

(This article belongs to the Section Biological Factors)

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