Biomolecules

23 pages, 4882 KB

Open AccessEditor’s ChoiceArticle

Integrative Multimodal Profiling of TAp73 and DNp73 Reveals Isoform-Specific Transcriptomic Coregulator Landscapes in Cancer Programs

by Steffen Möller, Alf Spitschak, Nico Murr and Brigitte M. Pützer

Biomolecules 2026, 16(1), 63; https://doi.org/10.3390/biom16010063 - 31 Dec 2025

Viewed by 928

Abstract

(1) Background: The transcription factor p73 exists in multiple isoforms with divergent functions in cancer. While DNp73 promotes stemness, epithelial–mesenchymal transition (EMT), and metastasis, the tumor-suppressive isoform TAp73 can also switch to promoting cancer progression. How isoforms sharing the same DNA-binding domain produce [...] Read more.

(1) Background: The transcription factor p73 exists in multiple isoforms with divergent functions in cancer. While DNp73 promotes stemness, epithelial–mesenchymal transition (EMT), and metastasis, the tumor-suppressive isoform TAp73 can also switch to promoting cancer progression. How isoforms sharing the same DNA-binding domain produce divergent outcomes remains unclear. (2) Methods: Here, we performed CUT&RUN in combination with JASPAR, transcriptomics, proteomics, patient survival and gene expression data to map genome-wide and promoter-associated DNA-binding and coregulatory transcription factor (coTF) profiles of TAp73α and DNp73β in melanoma cells. (3) Results: Systematic screening for motif enrichment in cancer hallmark gene sets revealed TAp73- and DNp73-specific coTF repertoires with distinct functions. We identified a coregulator signature for EMT genes enriched for both isoforms that has tumor context-dependent effects on survival and correlates with unfavorable patient prognosis. Of these EMT-associated coTFs, PATZ1 was validated as a novel direct interactor of DNp73β. (4) Conclusions: Our results provide a comprehensive reference map of p73 isoform-specific binding and coregulator recruitment and establish a workflow to model their influence on cancer reprogramming with implications for AI-based individualized therapy. Full article

(This article belongs to the Special Issue p53 Family: The Molecular Landscape in Cancer and Beyond)

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21 pages, 4292 KB

Open AccessEditor’s ChoiceArticle

Intermethod Characterization of Commercially Available Extracellular Vesicles as Reference Materials

by Sumeet Poudel, Diane L. Nelson, James H. Yen, Yuefan Wang, Hui Zhang, Zhiyong He, Ashley Beasley Green, Wyatt N. Veerland, Thomas E. Cleveland IV IV, Sean E. Lehman, Kurt D. Benkstein, Bryant C. Nelson and Lili Wang

Biomolecules 2026, 16(1), 66; https://doi.org/10.3390/biom16010066 - 31 Dec 2025

Cited by 3 | Viewed by 1353

Abstract

The National Institute of Standards and Technology (NIST) is developing analytical methods to characterize extracellular vesicles (EVs) to support the urgent need for standardized EV reference materials (RMs). This study used orthogonal techniques, cryogenic electron microscopy (Cryo-EM), particle tracking analysis (PTA), asymmetrical flow [...] Read more.

The National Institute of Standards and Technology (NIST) is developing analytical methods to characterize extracellular vesicles (EVs) to support the urgent need for standardized EV reference materials (RMs). This study used orthogonal techniques, cryogenic electron microscopy (Cryo-EM), particle tracking analysis (PTA), asymmetrical flow field-flow fractionation (AF⁴), and microfluidic resistive pulse sensing (MRPS), to evaluate particle size distributions (PSDs) and particle number concentrations (PNCs) of human mesenchymal stem cells (MSCs) and LNCaP prostate cancer cell EVs. Proteomic profiles were assessed by mass spectrometry (MS), and microRNA (miRNA) content of LNCaP EVs was evaluated by small RNA-seq at two independent laboratories. A commercial green fluorescent protein exosome served as a control, except in Cryo-EM, proteomic, and miRNA analyses. Cryo-EM, regarded as the gold standard for morphological resolution, served as PSD reference. PSDs from all methods skewed larger than Cryo-EM, with MRPS closest, AF⁴ most divergent, and PTA intermediate with broader distributions. All techniques reported broad PSDs (30 nm to >350 nm) with PNCs decreasing with increasing particle size, except for AF⁴. Quantitative discrepancies in PNCs reached up to two orders of magnitude across methods and cell sources. MS identified global and EV-specific proteins, including syntenin-1 and tetraspanins CD9, CD63, and CD81. RNA-seq revealed notable inter-laboratory variation. These findings highlight the variability across measurement platforms and emphasize the need for reproducible methods to support NIST’s mission of developing reliable EV reference materials. Full article

(This article belongs to the Section Cellular Biochemistry)

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24 pages, 1760 KB

Open AccessEditor’s ChoiceReview

How Adipocytes Orchestrate Inflammation Within Adipose Tissue?

by Romane Higos, Gianluca Renzi, Paul Taillandier, Fatiha Merabtene, Christine Rouault, Jimon Boniface Abatan, Mélanie Lambert, Isabelle Dugail, Karine Clément, Geneviève Marcelin, Salwan Maqdasy, Christophe Breton and Simon Lecoutre

Biomolecules 2026, 16(1), 59; https://doi.org/10.3390/biom16010059 - 30 Dec 2025

Cited by 3 | Viewed by 1324

Abstract

Adipose tissue is far more than a passive reservoir for surplus energy: it is an active metabolic and endocrine organ that senses nutrient availability and orchestrates systemic energy balance. When caloric intake chronically exceeds expenditure, adipocytes become engorged with lipids and exposed to [...] Read more.

Adipose tissue is far more than a passive reservoir for surplus energy: it is an active metabolic and endocrine organ that senses nutrient availability and orchestrates systemic energy balance. When caloric intake chronically exceeds expenditure, adipocytes become engorged with lipids and exposed to metabolic, mechanical, and hypoxic stress. To adapt, they initiate a fibro-inflammatory response that may be protective in the short term. As this response becomes chronic, adipocytes lose their metabolic flexibility, acquire a maladaptive fibro-inflammatory phenotype, and contribute to the cascade of inflammation, insulin resistance, and metabolic disease that characterizes obesity. In this review, we dissect the cellular and molecular cues that trigger fibro-inflammation, from nutrient excess and mitochondrial stress to hypoxia and immunometabolic rewiring, and highlight how these processes reshape adipocyte identity and tissue homeostasis. Full article

(This article belongs to the Section Molecular Biology)

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17 pages, 2250 KB

Open AccessEditor’s ChoiceArticle

Latent Toxoplasma gondii Infection Does Not Modulate Immune Aging in a Cross-Sectional Working-Age Population Study

by Peter Bröde, Maren Claus, Stephan Getzmann, Klaus Golka, Jan G. Hengstler, Jörg Reinders, Edmund Wascher, Carsten Watzl and Patrick D. Gajewski

Biomolecules 2026, 16(1), 55; https://doi.org/10.3390/biom16010055 - 30 Dec 2025

Viewed by 824

Abstract

Latent, i.e., asymptomatic Toxoplasma gondii (T. gondii) infection might accelerate or modulate the aging process of cognitive and sensory functions involving pro-inflammatory immune responses. For evaluating a potential role of latent T. gondii infection in immunological aging, we determined T. gondii [...] Read more.

Latent, i.e., asymptomatic Toxoplasma gondii (T. gondii) infection might accelerate or modulate the aging process of cognitive and sensory functions involving pro-inflammatory immune responses. For evaluating a potential role of latent T. gondii infection in immunological aging, we determined T. gondii antibody levels and immunosenescence biomarkers in a cross-sectional sample of 584 volunteers aged 20–70 years from the Dortmund Vital Study (ClinicalTrials.gov Identifier NCT05155397) representing the regional population. One-hundred-sixty-one participants were seropositive, representing an overall 28% latent T. gondii seroprevalence, which did not significantly differ between males and females, but increased with age. Consequently, seropositive individuals were older than the seronegative participants. Latent T. gondii infection exhibited significant bivariate associations with the composite immune age index IMMAX pointing to accelerated immune aging in seropositive individuals. In addition, IMMAX increased with age and in males. However, associations of latent T. gondii infection with immunosenescence biomarkers disappeared when adjusting the analyses for sex and age. Moreover, the non-significant interaction between T. gondii status and age when predicting biomarker levels indicated that latent T. gondii infection did not modify the immunosenescence trend. Summarized, our results suggest that latent T. gondii infection is unlikely to modulate immune aging concerning cellular senescence in otherwise healthy working-age adults. Full article

(This article belongs to the Section Molecular Biomarkers)

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19 pages, 16108 KB

Open AccessEditor’s ChoiceArticle

Dodecanedioic Acid: Alternative Carbon Substrate or Toxic Metabolite?

by Igor Radzikh, Usua Oyarbide, Akshay Suresh Patil and Yana I. Sandlers

Biomolecules 2026, 16(1), 57; https://doi.org/10.3390/biom16010057 - 30 Dec 2025

Cited by 1 | Viewed by 1007

Abstract

Twelve-carbon dicarboxylic acid dodecanedioic acid (DODA) has gained recent interest as an alternative nutrient. However, little is known about DODA cellular metabolism. Our study presents novel data on DODA metabolism and its potential role as an alternative carbon substrate. Cells are readily oxidizing [...] Read more.

Twelve-carbon dicarboxylic acid dodecanedioic acid (DODA) has gained recent interest as an alternative nutrient. However, little is known about DODA cellular metabolism. Our study presents novel data on DODA metabolism and its potential role as an alternative carbon substrate. Cells are readily oxidizing DODA as a primary carbon source, yielding acetyl-CoA and succinate and replenishing the Krebs cycle. Furthermore, cells treated with DODA are characterized by a distinct metabolic profile, whereas pathways associated with energy metabolism are highly impacted. We also found that DODA administration alters carbon substrate preferences for respiration, restricting overreliance on one substrate as a primary fuel. Consequently, by rebalancing cellular energy metabolism, DODA as a supplemental carbon source may have significant therapeutic implications in conditions that are characterized by energy deficiency and metabolic inflexibility. Full article

(This article belongs to the Topic Bioactive Compounds with Application Potentials in Nutraceuticals and Nutricosmetics: Focus on Mechanism of Action and Application Science—2nd Edition)

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16 pages, 3513 KB

Open AccessEditor’s ChoiceArticle

Melatonin Administration Attenuates High-Fat-Diet-Induced Renal Damage in Wistar Rats

by Olesia Kalmukova, Anastasiia Zavora, Alena Cherezova, Olexiy Savchuk, Mariia Stefanenko, Mykhailo Fedoriuk, Adam C. Jones, Valentyn Nepomnyashchy, Mykola Dzerzhynskyi, Marharyta Semenikhina, Daria V. Ilatovskaya and Oleg Palygin

Biomolecules 2026, 16(1), 36; https://doi.org/10.3390/biom16010036 - 25 Dec 2025

Cited by 1 | Viewed by 888

Abstract

Obesity is a major contributor to kidney injury, in part through circadian rhythms disruption and oxidative stress. Melatonin, a circadian clock regulator, has been proposed as a protective agent against metabolic and renal complications. We investigated the effects of chronic melatonin supplementation on [...] Read more.

Obesity is a major contributor to kidney injury, in part through circadian rhythms disruption and oxidative stress. Melatonin, a circadian clock regulator, has been proposed as a protective agent against metabolic and renal complications. We investigated the effects of chronic melatonin supplementation on kidney injury and circadian regulation in a rat obesity model. We hypothesized that melatonin administration ameliorates kidney injury induced by a high-calorie diet. Male Wistar rats were fed a normal or hypercaloric diet for six weeks, followed by seven weeks of vehicle or melatonin treatment (30 mg/kg/day in drinking water); biometric parameters and renal injury were assessed. Obese rats exhibited increased visceral adiposity, elevated resistin, renal hypertrophy, fibrosis, tubular degeneration, and glomerular injury, accompanied by higher KIM-1 levels. Melatonin attenuated renal fibrosis, reduced KIM-1, TGFβ, and TNFR1 levels, improved proximal tubule and glomerular damage, and lowered adipose TNF-α levels in the obese groups. In lean controls, melatonin increased nuclear BMAL1 levels, while in obese rats this effect was blunted; of note, BMAL1 accumulated in distal tubular cytoplasm in both melatonin-treated groups. These findings suggest that melatonin mitigates obesity-induced renal pathology through anti-fibrotic inflammation-related mechanisms, while also revealing a novel link between circadian disruption and kidney injury. Our results support melatonin as a therapeutic agent for obesity-related renal disease. Full article

(This article belongs to the Special Issue Melatonin in Normal Physiology and Disease, 2nd Edition)

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25 pages, 3920 KB

Open AccessEditor’s ChoiceArticle

Effect of the Icelandic Mutation APP^A673T in the Murine APP Gene on Phenotype of Line 66 Tau Mice

by Anne Anschuetz, Lianne Robinson, Miguel Mondesir, Valeria Melis, Bettina Platt, Charles R. Harrington, Gernot Riedel and Karima Schwab

Biomolecules 2026, 16(1), 28; https://doi.org/10.3390/biom16010028 - 24 Dec 2025

Cited by 1 | Viewed by 770

Abstract

The Icelandic mutation in the amyloid precursor protein (APP), APP^A673T, has been identified in Icelandic and Scandinavian populations and is associated with a significantly lower risk of developing Alzheimer’s disease (AD). The introduction of the human APP^A673T form led to [...] Read more.

The Icelandic mutation in the amyloid precursor protein (APP), APP^A673T, has been identified in Icelandic and Scandinavian populations and is associated with a significantly lower risk of developing Alzheimer’s disease (AD). The introduction of the human APP^A673T form led to a reduction in amyloid β-protein (Aβ) production and tau pathology, but the effect of mouse APP^A673T on tau and Aβ pathology is not well studied. We have crossed line 66 (L66) tau transgenic mice that overexpress the P301S aggregation-prone form of tau with C57Bl6/J mice expressing a single-point mutation edited into the murine APP gene via CRISPR-Cas gene editing, known as mAPP^A673T. We have performed ELISA, histopathological, and behavioural analyses of heterozygous male/female L66 and L66 xmAPP^A673T crosses at the age of 6 months to investigate the effect of the murine A673T mutation on tau brain pathology and behavioural deficits in these mice. Using immunohistochemistry, we found only a moderate, yet significant, reduction in mAb 7/51-reactive tau for female L66 x mAPP^A673T compared to L66 mice. Quantification of tau in soluble/insoluble brain homogenate fractions by ELISA confirmed the lack of overt differences between genotypes, as did our extensive behavioural phenotyping using six different paradigms assessing motor function, olfaction, depression/apathy-like behaviour, as well as exploration and sociability. Therefore, the mAPP^A673T mutation has a moderate impact on tau pathology but does not appear to impact motor and neuropsychiatric behaviour in L66 tau transgenic mice. Full article

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

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30 pages, 1996 KB

Open AccessEditor’s ChoiceReview

Electrochemical Choline Sensing: Biological Context, Electron Transfer Pathways and Practical Design Strategies

by Angel A. J. Torriero, Sarah M. Thiak and Ashwin K. V. Mruthunjaya

Biomolecules 2026, 16(1), 23; https://doi.org/10.3390/biom16010023 - 23 Dec 2025

Cited by 1 | Viewed by 649

Abstract

Choline is a central metabolite that connects membrane turnover, neurotransmission, and one-carbon metabolism, and its reliable measurement across diverse biological matrices remains a significant analytical challenge. This review brings together biological context, electrochemical mechanisms, and device engineering to define realistic performance targets for [...] Read more.

Choline is a central metabolite that connects membrane turnover, neurotransmission, and one-carbon metabolism, and its reliable measurement across diverse biological matrices remains a significant analytical challenge. This review brings together biological context, electrochemical mechanisms, and device engineering to define realistic performance targets for choline sensors in blood, cerebrospinal fluid, extracellular space, and milk. We examine enzymatic sensor architectures ranging from peroxide-based detection to mediated electron transfer via ferrocene derivatives, quinones, and osmium redox polymers and assess how applied potential, oxygen availability, and film structure shape electron-transfer pathways. Evidence for direct electron transfer with choline oxidase is critically evaluated, with emphasis on the essential controls needed to distinguish true flavin-based communication from peroxide-related artefacts. We also examine bienzymatic formats that allow operation at low or negative bias and discuss strategies for matrix-matched validation, selectivity, drift control, and resistance to fouling. To support reliable translation, we outline reporting standards that include matrix-specific concentration ranges, reference electrode notation, mediator characteristics, selectivity panels, and access to raw electrochemical traces. By connecting biological requirements to mechanistic pathways and practical design considerations, this review provides a coherent framework for developing choline sensors that deliver stable, reproducible performance in real samples. Full article

(This article belongs to the Section Chemical Biology)

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31 pages, 5560 KB

Open AccessEditor’s ChoiceReview

Structural and Computational Insights into the Angiotensin II Type 1 Receptor: Advances in Antagonist Design and Implications for Hypertension Therapy (2020–2024)

by Filippos Panteleimon Chatzipieris, Errikos Petsas, George Lambrinidis, John M. Matsoukas and Thomas Mavromoustakos

Biomolecules 2026, 16(1), 20; https://doi.org/10.3390/biom16010020 - 22 Dec 2025

Cited by 1 | Viewed by 1068

Abstract

The renin–angiotensin–aldosterone system (RAAS) is essential for controlling blood pressure and maintaining fluid balance, driving significant structural changes throughout the cardiovascular system, including the heart and blood vessels. As a result, the RAAS is a key therapeutic target for various chronic cardiovascular diseases, [...] Read more.

The renin–angiotensin–aldosterone system (RAAS) is essential for controlling blood pressure and maintaining fluid balance, driving significant structural changes throughout the cardiovascular system, including the heart and blood vessels. As a result, the RAAS is a key therapeutic target for various chronic cardiovascular diseases, ranging from arterial hypertension (AH) to heart failure (HF). In this review, one of our objectives is to describe the new evidence over the last 4 years regarding the RAAS. Moreover, we pay attention to the structure and function of the angiotensin II type 1 receptor (AT1R) and its role in hypertension, as well as define its active site. Later, we discuss the most potent, selective inhibitors of AT1 receptors, based on in vitro and in vivo experiments, from 2020 to 2024. Large peptide molecules, small non-peptide-like molecules, and sartan derivatives are analyzed. The low IC₅₀ values of the entities that do not resemble sartans showcase the vast chemical space that can be explored for the creation of more potent antihypertensive medications. We have also employed computational chemistry tools in order to identify key molecular interactions between the compounds of the literature studied in order to elucidate the underlying reasons why these different molecules exhibit variations in their binding energies and overall potency. Full article

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

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14 pages, 2432 KB

Open AccessEditor’s ChoiceReview

Parental Histone Recycling During Chromatin Replication

by Xin Bi

Biomolecules 2026, 16(1), 13; https://doi.org/10.3390/biom16010013 - 20 Dec 2025

Cited by 1 | Viewed by 1013

Abstract

The past decade has seen significant advancement in our understanding of DNA replication-coupled chromatin assembly, especially parental histone recycling that is essential for epigenetic inheritance. Leading strand-specific and lagging strand-specific pathways have been found to promote the transfer of parental histones H3-H4 to [...] Read more.

The past decade has seen significant advancement in our understanding of DNA replication-coupled chromatin assembly, especially parental histone recycling that is essential for epigenetic inheritance. Leading strand-specific and lagging strand-specific pathways have been found to promote the transfer of parental histones H3-H4 to nascent DNA. It is now clear that the replisome initially characterized as the machinery that carries out the duplication of genomic DNA is also responsible for parental histone recycling. A series of replisome components including CMG (Cdc45-MCM-GINS) replicative helicase, DNA polymerases Polε, Polδ, Polα-primase, and FPC (Fork Protection Complex) that promote parental histone recycling exhibit histone-binding activities. Structural analyses of native and reconstituted replisomes, together with AlphaFold modeling of histone (H3-H4)₂ tetramer binding by replisome components, provided a framework for understanding the molecular mechanisms of parental histone recycling. A working model has emerged in which the mobile histone chaperone FACT (Facilitates Chromatin Transcription) binds parental histone (H3-H4)₂ tetramer or (H3-H4)₂-(H2A-H2B) hexamer on the front of the replication fork, and escorts it across the replisome to the daughter strands in the wake of the replication fork. In this model, parental histones transiently associate with the histone-binding modules in the replisome as steppingstones during their movement. Future studies are needed to elucidate the spatiotemporal coordination of the functions of replisome factors in parental histone transfer. Full article

(This article belongs to the Special Issue Recent Advances in Chromatin and Chromosome Molecular Research)

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21 pages, 6422 KB

Open AccessEditor’s ChoiceArticle

Generation of Bioactive Stem Cell-Derived Secretome in 3D Bioreactor System: Towards Cell-Free Therapy in Veterinary Medicine

by Věra Daňková, Andrea Exnerová, Hana Vágnerová, Vojtěch Pavlík and Kristina Nešporová

Biomolecules 2026, 16(1), 2; https://doi.org/10.3390/biom16010002 - 19 Dec 2025

Cited by 3 | Viewed by 929

Abstract

Canine adipose-derived mesenchymal stem cells (cASC) are promising for regenerative veterinary medicine due to their immunomodulatory and reparative capacities. Three-dimensional (3D) culturing provides a more physiologically relevant environment than conventional two-dimensional (2D) monolayers, enhancing paracrine activity and therapeutic potential of mesenchymal stem cells [...] Read more.

Canine adipose-derived mesenchymal stem cells (cASC) are promising for regenerative veterinary medicine due to their immunomodulatory and reparative capacities. Three-dimensional (3D) culturing provides a more physiologically relevant environment than conventional two-dimensional (2D) monolayers, enhancing paracrine activity and therapeutic potential of mesenchymal stem cells (MSC). This study investigates the production and biological characterization of cASC secretome generated under hypoxic conditions with platelet lysate (PLT) supplementation, either in a 2D culture or in a stirred-tank 3D culture. Secretomes obtained from 3D cultures were compared with those from 2D cultures prepared under identical hypoxic and PLT-supplemented conditions. Quantitative analyses revealed enhanced secretion of key factors, including monocyte chemoattractant protein-1 (MCP-1) and vascular endothelial growth factor (VEGF), in 3D-derived secretomes. Functional in vitro assays demonstrated superior anti-inflammatory, pro-migratory, and antifibrotic effects of the 3D secretome, evidenced by nuclear factor kappa B (NF-κB) inhibition, increased fibroblast migration, and modulation of extracellular matrix gene expression. Additionally, the bioreactor system enabled consistent secretome production with reproducible biological activity. These findings indicate that 3D bioreactor cultivation under hypoxia with PLT supplementation can generate a biologically active secretome from canine adipose-derived stem cells, providing a promising basis for further exploration in veterinary regenerative applications. Full article

(This article belongs to the Section Molecular Medicine)

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16 pages, 2734 KB

Open AccessEditor’s ChoiceArticle

Metabolomic Profiling Reveals Brain Lipid Alterations in PEX7-Deficient Models of Rhizomelic Chondrodysplasia Punctata

by Riya Sankhe, Meredith I. Williams, Wedad Fallatah, Laura Mackay, Mary Layne Brown, Pranjali Bhagwat, Sarah H. Elsea, Nancy Braverman and Michael F. Wangler

Biomolecules 2026, 16(1), 6; https://doi.org/10.3390/biom16010006 - 19 Dec 2025

Cited by 1 | Viewed by 842

Abstract

Rhizomelic chondrodysplasia punctata type 1 (RCDP1) is a peroxisomal disorder characterized by skeletal shortening, intellectual disability, seizures, cataracts, and reduced lifespans. RCDP1 is caused by biallelic loss-of-function variants in PEX7, which encodes a protein required for importing select enzymes into the peroxisome [...] Read more.

Rhizomelic chondrodysplasia punctata type 1 (RCDP1) is a peroxisomal disorder characterized by skeletal shortening, intellectual disability, seizures, cataracts, and reduced lifespans. RCDP1 is caused by biallelic loss-of-function variants in PEX7, which encodes a protein required for importing select enzymes into the peroxisome matrix, including those essential for ether lipid synthesis (e.g., plasmalogens) and the branched-chain fatty acid catabolism. Plasmalogen deficiency is a hallmark of RCDP1 and other peroxisomal disorders, including RCDP types 2-5 (RCDP2-5) and Zellweger spectrum disorders (ZSD). Here, we performed comprehensive metabolomic profiling of clinical samples from RCDP patients and Pex7-deficient mouse models. We identified profound neurometabolic disturbances in the cerebral cortex and cerebellum of Pex7-deficient mice involving multiple lipid classes, including phosphatidylethanolamines (PEs), phosphatidylcholines (PCs), acylcarnitines, and sphingomyelins. Notably, many of these neurometabolic alterations were absent in patient and Pex7-deficient mouse plasma, indicating that plasma-based profiling can underrepresent the extent of CNS lipid remodeling. Overall, these findings reveal novel insights into neurometabolic adaptations to plasmalogen deficiency and suggest the potential involvement of additional pathways that may contribute to neurological dysfunction in RCDP. Full article

(This article belongs to the Section Molecular Medicine)

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23 pages, 1253 KB

Open AccessFeature PaperEditor’s ChoiceReview

Advances in Bioactive Compounds from Plants and Their Applications in Alzheimer’s Disease

by Steve Pavlov, Santosh Kumar Prajapati, Dhananjay Yadav, Andrea Marcano-Rodriguez, Hariom Yadav and Shalini Jain

Biomolecules 2026, 16(1), 7; https://doi.org/10.3390/biom16010007 - 19 Dec 2025

Cited by 3 | Viewed by 2533

Abstract

Alzheimer’s disease (AD), the leading cause of dementia worldwide, is characterized by progressive neuronal loss, amyloid-β (Aβ) aggregation, tau hyperphosphorylation, oxidative stress, neuroinflammation, cholinergic dysfunction, and gut–brain axis dysregulation. Despite advances in anti-amyloid therapeutics, current interventions provide only modest symptomatic relief and face [...] Read more.

Alzheimer’s disease (AD), the leading cause of dementia worldwide, is characterized by progressive neuronal loss, amyloid-β (Aβ) aggregation, tau hyperphosphorylation, oxidative stress, neuroinflammation, cholinergic dysfunction, and gut–brain axis dysregulation. Despite advances in anti-amyloid therapeutics, current interventions provide only modest symptomatic relief and face limitations in accessibility, cost, and long-term efficacy. Plant-derived bioactive compounds, rooted in traditional medicine systems such as Ayurveda and Traditional Chinese Medicine, have gained increasing attention as multi-target therapeutic agents due to their pleiotropic actions, relative safety, and ability to cross the blood–brain barrier. This review synthesizes mechanistic and translational evidence on major phytochemicals, including withanolides (Withania somnifera), curcumin (Curcuma longa), ginkgolides and bilobalide (Ginkgo biloba), bacosides (Bacopa monnieri), ginsenosides (Panax ginseng), crocin/safranal (Crocus sativus), epigallocatechin-3-gallate (Camellia sinensis), rosmarinic acid (Salvia officinalis, Melissa officinalis), and asiaticosides (Centella asiatica). These compounds exert neuroprotective effects by inhibiting Aβ aggregation, reducing tau phosphorylation, scavenging reactive oxygen species, attenuating NF-κB-mediated inflammation, modulating cholinergic signaling, enhancing synaptic plasticity via brain-derived neurotrophic factor/cAMP response element-binding protein (BDNF/CREB) activation, and regulating gut microbiota. Multi-target approach analyses underscore their synergistic potential in targeting interconnected AD pathways. However, translation remains hindered by poor oral bioavailability, rapid metabolism, and variability in clinical outcomes. Advances in delivery platforms, including liposomes, bilosomes, solid lipid nanoparticles, and nanostructured lipid carriers, are improving stability, blood–brain penetration, and therapeutic efficacy in preclinical models. Collectively, plant-derived phytochemicals serve as promising, affordable, and multi-modal candidates for reshaping AD management, bridging traditional knowledge with modern therapeutic innovation. Full article

(This article belongs to the Special Issue Targeting Protein Misfolding: From Alzheimer's Amyloids to Therapeutic Peptides)

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17 pages, 1950 KB

Open AccessEditor’s ChoiceArticle

Talaporfin Sodium as a Clinically Translatable Radiosensitizer in Radiodynamic Therapy

by Junko Takahashi, Junkoh Yamamoto, Kohei Suzuki, Shohei Nagasaka, Kaizhen Yang, Haobo Zhao and Teppei Yamaoka

Biomolecules 2025, 15(12), 1748; https://doi.org/10.3390/biom15121748 - 18 Dec 2025

Cited by 1 | Viewed by 802

Abstract

Talaporfin sodium (mono-L-aspartyl chlorin e6; NPe6), a second-generation photosensitizer, is clinically used in photodynamic therapy (PDT). It accumulates preferentially in tumors and exhibits deep tissue penetration, rapid systemic clearance, and minimal photosensitivity. However, treatment of deep-seated malignancies remains challenging. Here, we demonstrate that [...] Read more.

Talaporfin sodium (mono-L-aspartyl chlorin e6; NPe6), a second-generation photosensitizer, is clinically used in photodynamic therapy (PDT). It accumulates preferentially in tumors and exhibits deep tissue penetration, rapid systemic clearance, and minimal photosensitivity. However, treatment of deep-seated malignancies remains challenging. Here, we demonstrate that talaporfin sodium undergoes physicochemical reactions with X-rays to generate reactive oxygen species, a mechanism analogous to that of 5-aminolevulinic acid (5-ALA)-induced protoporphyrin IX in radiodynamic therapy (RDT). To evaluate its therapeutic efficacy, we employed a pancreatic cancer xenograft model using MIA PaCa-2 cells in mice. Talaporfin sodium was administered intravenously 2 h before X-ray exposure, followed by fractionated X-ray irradiation (3 Gy daily for 3 consecutive days). Talaporfin-mediated RDT significantly inhibited tumor growth compared with radiation therapy alone. Furthermore, an exploratory RNA-seq analysis of xenografts revealed transcriptional signatures of stress and immune activation, suggesting that talaporfin-mediated RDT enhances oxidative and immunogenic responses within the tumor microenvironment. These findings highlight the potential of talaporfin sodium as a clinically translatable radiosensitizer for RDT, offering a promising strategy for the treatment of deep-seated cancers such as pancreatic carcinoma. Full article

(This article belongs to the Section Chemical Biology)

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19 pages, 7178 KB

Open AccessEditor’s ChoiceArticle

Humanized Bone Model Identifies BMP6 as a Multifunctional Regulator in Myeloma Bone Disease

by Jiaxian Wang, Thomas Baardemans, Ricardo de Matos Simoes, Willy Noort, Ruud W. J. Ruiter, Henk-Jan Prins, Susan E. van Hal-van Veen, Huipin Yuan, Joost D. de Bruijn, Anton C. M. Martens, Constantine S. Mitsiades, Sonja Zweegman, Maria Themeli and Richard W. J. Groen

Biomolecules 2025, 15(12), 1747; https://doi.org/10.3390/biom15121747 - 18 Dec 2025

Cited by 1 | Viewed by 998

Abstract

Multiple myeloma (MM) is a plasma cell malignancy that disrupts bone homeostasis by suppressing osteogenesis and promoting osteoclast activity. While most therapeutic interventions to date have focused on targeting tumor cells and reducing osteolysis, we investigate whether osteoinductive strategies can restore bone formation [...] Read more.

Multiple myeloma (MM) is a plasma cell malignancy that disrupts bone homeostasis by suppressing osteogenesis and promoting osteoclast activity. While most therapeutic interventions to date have focused on targeting tumor cells and reducing osteolysis, we investigate whether osteoinductive strategies can restore bone formation and counteract disease progression. Using a human bone marrow-like scaffold model that enables direct in vivo evaluation of tumor–stroma interactions and human bone formation, we demonstrate that MM-derived mesenchymal stromal cells (MSCs) retain osteogenic potential but are functionally suppressed by MM cells. Transcriptomic profiling of MM-primed MSCs revealed the downregulation of small leucine-rich proteoglycans (SLRPs), ASPN, OGN, and OMD, key mediators of bone morphogenetic protein (BMP) signaling, which governs osteoblast differentiation. Among the BMPs analyzed, BMP6 emerged as a potent inducer of osteogenesis and regulator of the expression of these SLRPs. Notably, BMP6 selectively promoted bone formation without enhancing osteoclastogenesis and attenuated inflammatory and tumor-supportive MSC phenotypes. BMP6 also directly inhibited MM cell proliferation and suppressed IL6-induced growth. These findings highlight BMP6 as a distinct multifunctional regulator warranting further investigation as a potential therapeutic approach, while establishing the humanized model as a valuable platform for dissecting tumor–bone interactions in MM. Full article

(This article belongs to the Special Issue Multiple Myeloma: From Pathophysiology to Novel Therapeutic Approaches)

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31 pages, 1668 KB

Open AccessEditor’s ChoiceReview

Insulin Resistance at the Crossroads of Metabolic Inflammation, Cardiovascular Disease, Organ Failure and Cancer

by Amedeo Lonardo and Ralf Weiskirchen

Biomolecules 2025, 15(12), 1745; https://doi.org/10.3390/biom15121745 - 17 Dec 2025

Cited by 7 | Viewed by 7196

Abstract

Insulin resistance (IR) describes impaired hormone signaling that triggers compensatory homeostatic responses resulting in hyperinsulinemia, increased accumulation of fatty substrates, lipotoxicity, oxidative stress, inflammation, cell death and fibrosis in target tissues. These processes ultimately lead to organ dysfunction and predispose certain individuals to [...] Read more.

Insulin resistance (IR) describes impaired hormone signaling that triggers compensatory homeostatic responses resulting in hyperinsulinemia, increased accumulation of fatty substrates, lipotoxicity, oxidative stress, inflammation, cell death and fibrosis in target tissues. These processes ultimately lead to organ dysfunction and predispose certain individuals to various types of cancer. In this context, we will review the molecular pathogenesis and clinical significance of IR, its role in ‘metaflammation’, and the damage caused by IR in the pancreas, cardiovascular system, liver, and kidneys. Additionally, we will discuss principles of drug treatment for IR and outline a research agenda in this field. Full article

(This article belongs to the Special Issue Molecular Aspects of Diseases Origin and Development)

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26 pages, 5258 KB

Open AccessEditor’s ChoiceArticle

Systems-Level Integration of Multi-Omics Identifies Genetic Modifiers of TANGO2 Deficiency Disorder

by Manuel Airoldi, Heather Bondi, Veronica Remori, Silvia Carestiato, Giovanni Battista Ferrero, Alfredo Brusco and Mauro Fasano

Biomolecules 2025, 15(12), 1742; https://doi.org/10.3390/biom15121742 - 16 Dec 2025

Cited by 2 | Viewed by 1208

Abstract

TANGO2 deficiency disorder is a rare autosomal recessive disease (~100 cases reported worldwide). Despite being caused by loss-of-function variants in the TANGO2 gene, patients exhibit marked phenotypic variability, including intrafamilial differences among individuals carrying identical variants. To uncover potential modifier mechanisms influencing disease [...] Read more.

TANGO2 deficiency disorder is a rare autosomal recessive disease (~100 cases reported worldwide). Despite being caused by loss-of-function variants in the TANGO2 gene, patients exhibit marked phenotypic variability, including intrafamilial differences among individuals carrying identical variants. To uncover potential modifier mechanisms influencing disease severity, we developed an integrative Systems biology framework, combining exome sequencing, transcriptomics, variant effect prediction, and Human Phenotype Ontology mapping. This approach was applied to two siblings carrying identical compound heterozygous TANGO2 variants but opposite clinical outcomes: one severely affected and one asymptomatic. Personalized protein–protein interaction networks and combined univariate and multivariate analyses were employed to maximize specificity in this single-family comparison. In the affected sibling, a cumulative burden of common APOB variants, together with altered VLDLR, NTN1, and LDHA expression, implicated disrupted lipid metabolism and neurodevelopmental pathways. The asymptomatic sibling harbored a potentially protective 3′-UTR variant in EP300 and no APOB variant burden, supporting enhanced post-transcriptional regulation within developmental biology networks. These findings highlight lipid metabolism as a key pathway in TANGO2 deficiency pathophysiology and suggest autophagy and mitophagy as additional modifier mechanisms influencing phenotypic variability. Our integrative multi-omics framework provides a valuable strategy for elucidating genotype-phenotype relationships in rare diseases and supports personalized therapeutic approaches. Full article

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

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27 pages, 4788 KB

Open AccessEditor’s ChoiceArticle

An Integrated Systems Pharmacology Approach Combining Bioinformatics, Untargeted Metabolomics and Molecular Dynamics to Unveil the Anti-Aging Mechanisms of Tephroseris flammea

by Min Hyung Cho, Haiyan Jin, JangHo Ha, SungJune Chu and SoHee An

Biomolecules 2025, 15(12), 1740; https://doi.org/10.3390/biom15121740 - 15 Dec 2025

Cited by 2 | Viewed by 898

Abstract

Skin aging, driven by oxidative stress, UV exposure, inflammation, and extracellular matrix degradation, necessitates the discovery of safer, multi-target natural products. We established an integrated pipeline combining UHPLC–MS/MS metabolomics, computational methods (network pharmacology, molecular docking, and dynamics simulation), and in vitro bioassays to [...] Read more.

Skin aging, driven by oxidative stress, UV exposure, inflammation, and extracellular matrix degradation, necessitates the discovery of safer, multi-target natural products. We established an integrated pipeline combining UHPLC–MS/MS metabolomics, computational methods (network pharmacology, molecular docking, and dynamics simulation), and in vitro bioassays to efficiently discover and mechanistically characterize anti-aging compounds from novel botanical sources. We applied this pipeline to identify and evaluate Tephroseris flammea, a previously unassessed plant. Metabolomic profiling identified 21 compounds, including flavonoids, phenylpropanoids, and pyrrolizidine alkaloids. These compounds were linked via network pharmacology to 226 skin-aging-related targets, primarily involving inflammation (via AKT1, RELA) and matrix degradation (via MAPK3). Molecular docking and 100 ns molecular dynamics simulations confirmed stable ligand-target interactions with favorable binding energies. Validating these in silico predictions, the T. flammea extract demonstrated significant antioxidant activity and effectively suppressed key inflammatory mediators (IL-6, TNF-α, COX-2) and MMP-1 levels in UVB-exposed fibroblasts, notably without significant cytotoxicity. Collectively, this study validates the utility of our pipeline to mechanistically characterize complex botanicals, revealing that T. flammea contains multifunctional compounds modulating critical inflammatory and matrix-regulatory cascades. This work validates our pipeline for identifying novel, mechanistically defined ingredients from complex botanical sources. Full article

(This article belongs to the Special Issue Research Progress on Anti-Aging with Natural Products)

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12 pages, 632 KB

Open AccessEditor’s ChoiceArticle

Malnutrition Is Associated with Increased Liver Stiffness in Type 2 Diabetes: The Mediating Role of Inflammation

by Aurelio Lo Buglio, Francesco Bellanti, Rosanna Villani, Cristiano Capurso, Grazia Pia Magnati, Sara Cioffi, Gabriele Tedesco, Carlo Alberto Torsello, Gianluigi Vendemiale and Gaetano Serviddio

Biomolecules 2025, 15(12), 1735; https://doi.org/10.3390/biom15121735 - 13 Dec 2025

Cited by 1 | Viewed by 875

Abstract

Background: Malnutrition is a prevalent and under-recognized condition in patients with type 2 diabetes mellitus (T2DM), contributing to various complications, including liver fibrosis. In this study, we aimed to evaluate the association between malnutrition and liver fibrosis in patients with T2DM, and to [...] Read more.

Background: Malnutrition is a prevalent and under-recognized condition in patients with type 2 diabetes mellitus (T2DM), contributing to various complications, including liver fibrosis. In this study, we aimed to evaluate the association between malnutrition and liver fibrosis in patients with T2DM, and to assess whether inflammation mediates this relationship. Methods: In this prospective single-centre study, 87 adult outpatients with T2DM underwent nutritional assessment using the Subjective Global Assessment (SGA) and liver stiffness measurement by transient elastography. Metabolic dysfunction-associated steatotic liver disease (MASLD) was diagnosed according to EASL guidelines. C-reactive protein (CRP) was measured as a marker of systemic inflammation. Multivariable linear regression and mediation analysis were performed, adjusting for age and sex. Results: Malnutrition was present in 50.6% of patients, MASLD in 66.7%, and both conditions coexisted in 36.8%. Malnutrition (B = 2.29, p < 0.001), MASLD (B = 1.54, p = 0.001), smoking (B = 1.06, p = 0.014), and CRP (B = 0.32, p < 0.001) were independently associated with increased liver stiffness. CRP partially mediated the effect of malnutrition on liver stiffness (indirect effect = 0.54; 95% CI 0.20–0.95), accounting for 18% of the total effect. Conclusions: In T2DM, malnutrition is a strong independent predictor of liver fibrosis, with its effect partially mediated by systemic inflammation. Addressing nutritional status and inflammatory burden may help slow fibrotic progression in this high-risk population. Full article

(This article belongs to the Special Issue Liver Damage and Associated Metabolic Disorders)

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13 pages, 2798 KB

Open AccessEditor’s ChoiceArticle

Yeast NatB Regulates Cell Death of Bax-Expressing Cells

by Joana P. Guedes, Filipa Mendes, Beatriz O. Machado, Stéphen Manon, Manuela Côrte-Real and Susana R. Chaves

Biomolecules 2025, 15(12), 1731; https://doi.org/10.3390/biom15121731 - 12 Dec 2025

Viewed by 767

Abstract

The pro-apoptotic protein Bax is a key apoptosis regulator, as its activity is the main driver of mitochondrial outer membrane permeabilization. Bax is therefore tightly regulated, both by protein–protein interactions and post-translational modifications, such as phosphorylation. Although less studied, N-terminal acetylation has also [...] Read more.

The pro-apoptotic protein Bax is a key apoptosis regulator, as its activity is the main driver of mitochondrial outer membrane permeabilization. Bax is therefore tightly regulated, both by protein–protein interactions and post-translational modifications, such as phosphorylation. Although less studied, N-terminal acetylation has also been implicated in Bax regulation: disruption of the NatB N-terminal acetyl transferase complex in both yeast and MEFs increases Bax mitochondrial localization, although increased translocation is not sufficient to trigger its activation. Using the well-established model of heterologous expression of human Bax in yeast, we further investigated its regulation by N-terminal acetylation. We found that the sensitivity of Bax-expressing cells to acetic acid is greatly enhanced in a strain lacking the yeast NatB catalytic subunit (Nat3p). We propose that the Bax-induced cell death process shifts to a regulated necrosis in this strain due to autophagy inhibition. Furthermore, we show that the protective role of Bcl-xL against acetic acid-induced cell death of Bax-expressing yeast cells requires Nat3p. We speculate that Nat3p modulates the function of pro-death and pro-survival proteins, ultimately affecting both the levels and mode of cell death. These findings may have implications for the development of novel therapeutic strategies targeting human diseases associated with cell death dysfunction. Full article

(This article belongs to the Section Biological Factors)

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19 pages, 5658 KB

Open AccessEditor’s ChoiceArticle

Aging Promotes Spontaneous Liver Injury: Insights from Metabolic, Inflammatory, and Fibrotic Pathways in C57BL/6 Mice

by Poonam Sagar, Sathish Kumar Perumal, Ramachandran Rajamanickam, Ramesh Bellamkonda, Sundararajan Mahalingam, Natalia A. Osna, Karuna Rasineni and Kusum K. Kharbanda

Biomolecules 2025, 15(12), 1727; https://doi.org/10.3390/biom15121727 - 11 Dec 2025

Cited by 1 | Viewed by 1136

Abstract

Aging is a critical factor influencing susceptibility to hepatic injury. In this study, the spontaneous development of liver injury with advancing age and potential sex-related differences in these processes are examined. This study focuses on key mechanisms such as fatty acid metabolism, immune [...] Read more.

Aging is a critical factor influencing susceptibility to hepatic injury. In this study, the spontaneous development of liver injury with advancing age and potential sex-related differences in these processes are examined. This study focuses on key mechanisms such as fatty acid metabolism, immune response, and cellular stress in male and female C57BL/6 mice. Aged male and female mice (20 to 22 months old) exhibited higher body weight and an altered metabolic profile and fatty acid metabolism compared to their younger counterparts (8 to 10 weeks old). In addition, increased oxidative stress, cellular senescence, expression of inflammatory markers, and cytokines/chemokines levels were also observed in aged male and female mice compared to younger mice. Furthermore, the aged mice exhibited increased indices of hepatic fibrosis, evident from the upregulation of smooth muscle actin-α, collagen, and transforming growth factor-β. In conclusion, aging promotes spontaneous liver injury by increasing indices of oxidative stress, steatosis, inflammation, and fibrosis. These results highlight the impact of chronological age on the liver that can increase its susceptibility to secondary hepatic stressors such as alcohol, high-calorie diet, or hepatotropic infections. Understanding how metabolic and inflammatory pathways change with aging in males and females is essential for elucidating the mechanisms that drive chronic liver disease progression. These insights are particularly important for developing targeted, sex-specific prevention and therapeutic strategies for the aging population. Full article

(This article belongs to the Section Molecular Medicine)

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19 pages, 576 KB

Open AccessEditor’s ChoiceArticle

Molecular Drivers of Vascular Adaptation in Young Athletes: An Integrative Analysis of Endothelial, Metabolic and Lipoprotein Biomarkers

by Jonas Haferanke, Lisa Baumgartner, Maximilian Dettenhofer, Stefanie Huber, Frauke Mühlbauer, Tobias Engl, Paulina Wasserfurth, Karsten Köhler, Renate Oberhoffer, Thorsten Schulz and Sebastian Freilinger

Biomolecules 2025, 15(12), 1726; https://doi.org/10.3390/biom15121726 - 11 Dec 2025

Cited by 2 | Viewed by 876

Abstract

Adolescence is a critical window for cardiovascular (CV) development, yet the molecular drivers of vascular adaptation to regular exercise in youth remain poorly understood. This cross-sectional study assessed vascular structure and function alongside endothelial, metabolic, and lipoprotein biomarkers in 203 healthy young athletes [...] Read more.

Adolescence is a critical window for cardiovascular (CV) development, yet the molecular drivers of vascular adaptation to regular exercise in youth remain poorly understood. This cross-sectional study assessed vascular structure and function alongside endothelial, metabolic, and lipoprotein biomarkers in 203 healthy young athletes (aged 10–16). Vascular phenotyping included carotid intima-media thickness (IMT), pulse wave velocity, and carotid deformation indices (strain, strain rate). Circulating nitric oxide (NO), endothelin-1, free triiodothyronine (fT3), leptin, low-density lipoprotein, and high-density lipoprotein were analyzed. Associations were examined using hierarchically adjusted multivariable linear regression, mediation and moderation were tested and sex-stratified/matched analyses were conducted. While training volume was not associated with endothelial markers, leptin was correlated positively with NO and negatively with diastolic strain rate, suggesting dual vascular actions. fT3 was inversely associated with IMT, indicating a potential protective role in vascular remodeling. Lipoprotein profiles showed no independent associations with vascular parameters. Hemodynamic load, particularly systolic blood pressure, emerged as the dominant determinant of arterial stiffness. Sex-specific differences across biomarkers and vascular indices support a multifactorial model: in active youth, vascular phenotype reflects hemodynamics, body composition, and endocrine–metabolic signals more than training; longitudinal mechanistic studies should clarify causal pathways and guide individualized cardiovascular risk profiling. Full article

(This article belongs to the Special Issue Biomolecular Sciences and Precision Medicine in Vascular Disease)

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18 pages, 2953 KB

Open AccessEditor’s ChoiceArticle

Enduring Effects of Humanin on Mitochondrial Systems in TBI Pathology

by Pavan Thapak, Zhe Ying and Fernando Gomez-Pinilla

Biomolecules 2025, 15(12), 1705; https://doi.org/10.3390/biom15121705 - 6 Dec 2025

Cited by 2 | Viewed by 1052

Abstract

Traumatic brain injury has long-term detrimental effects on neurological function and general quality of life of affected individuals. Bioenergetic failure is a primary mechanism for cellular dysfunction. We used the mitochondrial activator humanin (HN) to try to normalize the disruptive action of TBI [...] Read more.

Traumatic brain injury has long-term detrimental effects on neurological function and general quality of life of affected individuals. Bioenergetic failure is a primary mechanism for cellular dysfunction. We used the mitochondrial activator humanin (HN) to try to normalize the disruptive action of TBI on cellular bioenergetics in the hippocampus. We found that HN supplied right after the injury counteracted the action of TBI on metabolic sensing proteins (LKB1, AMPK, and AKT). HN also counteracted cognitive function and restored the synaptic proteins (Synapsin I and PSD-95) at three weeks post-injury. Moreover, HN normalized the disruptive action of TBI on mitochondrial functioning and dynamics (fusion, fission, and mitophagy). In addition, HN treatment counteracted TBI’s effects on mitochondrial biogenesis (PGC-1α), antioxidant (SOD2), and apoptotic marker (CC3). Furthermore, HN intervention in injured animals counteracted the gene expression linked with inflammation (Itgax, SALL1, GFAP, and NLRP3), synaptic plasticity (HDAC2), and bioenergetics (mtND2, TFAM, SIRT1, and SIRT3). These observations emphasize the therapeutic potential of HN by normalizing the fundamental aspects of TBI pathogenesis central to cellular bioenergetics and synaptic plasticity. Full article

(This article belongs to the Special Issue Advancing Molecular Regulation in Brain Injury Research: Mechanisms, Diagnosis, and Rehabilitation)

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30 pages, 4802 KB

Open AccessEditor’s ChoiceReview

It Takes Two to Tango: Current Understanding of the Role of M16 Family of Proteases and Their Structural Properties

by Miroslaw Jarzab and Joanna Skorko-Glonek

Biomolecules 2025, 15(12), 1697; https://doi.org/10.3390/biom15121697 - 5 Dec 2025

Viewed by 1169

Abstract

The M16 protease family comprises metalloendopeptidases, characterized by a unique molecular architecture. The active enzyme molecule is composed of two halves, which together form a structure resembling a clam shell. Although the active site residues are typically located in only one half, both [...] Read more.

The M16 protease family comprises metalloendopeptidases, characterized by a unique molecular architecture. The active enzyme molecule is composed of two halves, which together form a structure resembling a clam shell. Although the active site residues are typically located in only one half, both parts are essential for proper enzyme function. The M16 family includes many proteins that are crucial for the physiology of the organism and, therefore, are the subject of intensive research. The flagship examples are insulin-degrading enzyme (IDE), mitochondrial processing peptidases (MPPs), and mitochondrial and chloroplast presequence peptidases (PrePs). The substrates of these enzymes include many biologically important peptides, such as insulin and amyloid β. Therefore, M16 peptidases are considered attractive therapeutic targets, and understanding their structure and mechanism of action is essential for the development of specific and selective modulatory compounds. Full article

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

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27 pages, 3010 KB

Open AccessEditor’s ChoiceReview

Targeting the Reactive Proteome: Recent Advances in Activity-Based Protein Profiling and Probe Design

by Yuan-Fei Zhou, Ling Zhang, Zhuoyi L. Niu and Zhipeng A. Wang

Biomolecules 2025, 15(12), 1699; https://doi.org/10.3390/biom15121699 - 5 Dec 2025

Cited by 2 | Viewed by 3986

Abstract

Activity-based protein profiling (ABPP) has emerged as a powerful chemical proteomics approach for profiling active amino acid residues, mapping functional proteins, and guiding covalent drug development in complex biological systems. Recent methodological advances have produced several novel formats, including tandem orthogonal proteolysis-ABPP (TOP-ABPP), [...] Read more.

Activity-based protein profiling (ABPP) has emerged as a powerful chemical proteomics approach for profiling active amino acid residues, mapping functional proteins, and guiding covalent drug development in complex biological systems. Recent methodological advances have produced several novel formats, including tandem orthogonal proteolysis-ABPP (TOP-ABPP), isotopic tandem orthogonal proteolysis-ABPP (IsoTOP-ABPP), and competitive IsoTOP-ABPP, enabling broader target identification and quantitative analysis for varied experimental purposes. In parallel, chemical probe design has evolved to selectively target specific amino acid residues, such as cysteine (Cys), lysine (Lys), and histidine (His), and to incorporate photoaffinity labeling (PAL) functionalities for capturing transient or weak protein-ligand interactions. Additionally, the integration of cleavable linkers with diverse cleavage mechanisms, including acid/base-mediated, redox-mediated, and photo irradiation mechanisms, has enhanced probe versatility and downstream analytical workflows. This review summarizes recent advances in ABPP methodologies and the design of activity-based probes and PAL probes, emphasizing their implications for future work in chemical biology. Full article

(This article belongs to the Special Issue Advances and Novel Strategies for Studying Post-Translational Modifications (PTMs))

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28 pages, 1699 KB

Open AccessEditor’s ChoiceReview

The Role of Extracellular Proteases and Extracellular Matrix Remodeling in the Pre-Metastatic Niche

by Gillian C. Okura, Alamelu G. Bharadwaj and David M. Waisman

Biomolecules 2025, 15(12), 1696; https://doi.org/10.3390/biom15121696 - 5 Dec 2025

Cited by 3 | Viewed by 1850

Abstract

The premetastatic niche (PMN) represents a specialized microenvironment established in distant organs before the arrival of metastatic cells. This concept has fundamentally altered our understanding of cancer progression, shifting it from a random event-driven process to an orchestrated one. This review examines the [...] Read more.

The premetastatic niche (PMN) represents a specialized microenvironment established in distant organs before the arrival of metastatic cells. This concept has fundamentally altered our understanding of cancer progression, shifting it from a random event-driven process to an orchestrated one. This review examines the critical role of extracellular proteases in PMN formation, focusing on matrix metalloproteinases (MMPs), serine proteases, and cysteine cathepsins that collectively orchestrate extracellular matrix remodeling, immune modulation, and vascular permeability changes essential for metastatic colonization. Key findings demonstrate that MMP9 and MMP2 facilitate basement membrane degradation and the recruitment of bone marrow-derived cells. At the same time, tissue inhibitor of metalloproteinase-1 (TIMP-1) promotes organ-specific hepatic PMN recruitment through neutrophil recruitment mechanisms. The plasminogen–plasmin system emerges as a master regulator through its broad-spectrum proteolytic activity and ability to activate downstream proteases, with S100A10-mediated plasmin generation providing mechanistic pathways for remote PMN conditioning. Neutrophil elastase and cathepsin G contribute to the degradation of anti-angiogenic proteins, thereby creating pro-metastatic microenvironments. These protease-mediated mechanisms represent the earliest interventional window in metastatic progression, offering therapeutic potential to prevent niche formation rather than treat established metastases. However, significant methodological challenges remain, including the need for organ-specific biomarkers, improved in vivo methods for measuring protease activity, and a better understanding of temporal PMN dynamics across different target organs. Full article

(This article belongs to the Section Biological Factors)

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15 pages, 4357 KB

Open AccessEditor’s ChoiceArticle

Assessment of [¹²⁵I]a-Bungarotoxin Binding to a7 Nicotinic Acetylcholinergic Receptors in Hippocampus-Subiculum of Postmortem Human Parkinson’s Disease Brain

by Fariha Karim, Allyson Ngo, Titus E. Tucker, Ashlee D. L. Coronel and Jogeshwar Mukherjee

Biomolecules 2025, 15(12), 1686; https://doi.org/10.3390/biom15121686 - 2 Dec 2025

Viewed by 814

Abstract

Parkinson’s disease (PD) involves motor and cognitive impairment that nicotinic acetylcholine receptors (nAChRs) such as the α7 subtype are responsible for regulating. The hippocampus, abundant in α7 nAChRs, was quantitatively evaluated for [¹²⁵I]α-bungarotoxin ([¹²⁵I]α-Bgtx) binding to α7 nAChRs in [...] Read more.

Parkinson’s disease (PD) involves motor and cognitive impairment that nicotinic acetylcholine receptors (nAChRs) such as the α7 subtype are responsible for regulating. The hippocampus, abundant in α7 nAChRs, was quantitatively evaluated for [¹²⁵I]α-bungarotoxin ([¹²⁵I]α-Bgtx) binding to α7 nAChRs in postmortem human PD (n = 26; 12 male, 14 female) and cognitively normal (CN) (n = 29; 14 male, 15 female) brain slices. Anti-ubiquitin and anti-α-synuclein immunostained adjacent slices were analyzed using QuPath. Autoradiographs of [¹²⁵I]α-Bgtx radioligand binding were analyzed in OptiQuant. Ubiquitin and α-synuclein distribution generally aligned with the distribution of α7 nAChRs detected by [¹²⁵I]α-Bgtx. Binding of [¹²⁵I]α-Bgtx in PD cases was significantly greater than CN with a 32% increase in gray matter binding. A weak positive correlation between age and [¹²⁵I]α-Bgtx binding was found in both PD and CN. In comparison to Alzheimer’s disease hippocampus, [¹²⁵I]α-Bgtx binding in PD gray matter was higher by 41%. Differences in nAChR expression imply unique roles depending on the neurodegenerative pathology. PD may experience an increase in α7 nAChRs as a compensatory mechanism to the loss in neurons, highlighting its neuroprotective capabilities. [¹²⁵I]α-Bgtx shows potential as a radioligand for α7 nAChRs to elucidate the complexities of PD pathology. Full article

(This article belongs to the Special Issue New Discoveries in the Field of Neuropharmacology)

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34 pages, 1420 KB

Open AccessEditor’s ChoiceReview

The Neuro-Melanoma Singularity: Convergent Evolution of Neural and Melanocytic Networks in Brain Metastatic Adaptation

by Vlad-Petre Atanasescu, Alexandru Breazu, Stefan Oprea, Andrei-Ludovic Porosnicu, Anamaria Oproiu, Mugurel-Petrinel Rădoi, Octavian Munteanu and Cosmin Pantu

Biomolecules 2025, 15(12), 1683; https://doi.org/10.3390/biom15121683 - 2 Dec 2025

Cited by 1 | Viewed by 2052

Abstract

Melanoma cells in the brain may use similar mechanisms for adapting to injury and/or disease (that is, through continued reallocation of energy, matter, and information) as other cell types do to create an environment in which cancer cells can grow and sustain themselves [...] Read more.

Melanoma cells in the brain may use similar mechanisms for adapting to injury and/or disease (that is, through continued reallocation of energy, matter, and information) as other cell types do to create an environment in which cancer cells can grow and sustain themselves within the confines of the brain. These adaptable mechanisms include the ability to reactivate dormant neural crest-derived migration and communication pathways. Unlike some other types of cancers that invade neural tissue as a simple invasion, melanomas are capable of achieving limited molecular, metabolic, and electrical similarity to the neural circuitry of the brain. Melanomas achieve this limited similarity through both vascular co-optation and mimicking synaptic functions, as well as through their engagement of redox-coupled metabolic pathways and feedback-regulated signal transduction pathways. The result is the creation of a metastable tumor–host system, where the relationship between tumor and host is defined by the interaction of stabilizing and destabilizing forces; forces that define the degree of coherence, vulnerability, and persistence of the tumor–host system. In this review, we integrate molecular, electrophysiological, and anatomical data to develop a single unifying hypothesis for the functional integration of melanoma cells into the neural tissue of the brain. Additionally, we describe how neural crest-based regulatory pathways are reactivated in the adult brain and how tumor–host coherence is developed as a function of the shared thermodynamic and informational constraints placed on both tumor and host. We also describe how our proposed conceptual model allows for the understanding of therapeutic interventions as selective disruptions of the neural, metabolic, and immunological couplings that support metastatic adaptation. Full article

(This article belongs to the Special Issue Biomarkers and Therapeutic Approaches in Melanoma: New Omics-Strategies)

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15 pages, 3442 KB

Open AccessEditor’s ChoiceArticle

Transcriptomic Profiles from Stereo-EEGs May Reflect the Local Brain Cell Microenvironment in Human Epilepsy

by Julian Larkin, Anuj Kumar Dwivedi, Arun Mahesh, Albert Sanfeliu, Kieron J. Sweeney, Donncha F. O’Brien, Vijay K. Tiwari, Peter Widdess-Walsh and David C. Henshall

Biomolecules 2025, 15(12), 1684; https://doi.org/10.3390/biom15121684 - 2 Dec 2025

Viewed by 1120

Abstract

Background: Our understanding of the pathomechanisms of epilepsy has improved through techniques that access the living human brain. We recently reported that explanted stereo-electroencephalography (SEEG) electrodes from patients with epilepsy carry residual biomolecules and cells, which may be utilised for transcriptome and DNA [...] Read more.

Background: Our understanding of the pathomechanisms of epilepsy has improved through techniques that access the living human brain. We recently reported that explanted stereo-electroencephalography (SEEG) electrodes from patients with epilepsy carry residual biomolecules and cells, which may be utilised for transcriptome and DNA methylation profiling. Methods: Here, we applied bioinformatic and other analyses to explore the transcriptomes (RNA sequencing-based) of those SEEG cases to better understand the types of recovered transcripts in terms of representation of genes expressed by different cell types, brain structures, and the extent to which the signal may reflect local epileptiform activity. Results: Electrodes from all clinical cases retained protein-coding transcripts which reflected the local molecular microenvironment as well as epileptiform activity. Expression of genes involved in housekeeping functions, as well as markers of neuronal activity, was consistent between patients and between the electrode locations within the brain. We detected transcripts representing various cell types and subtypes, including excitatory and inhibitory neurons, all major classes of glia, and endothelial cells, as well as transcripts enriched in specific brain regions. Several genes showed a gradient of expression depending on the electrode position within the brain. We found examples of gene expression that correlated with epileptiform activity as recorded by SEEG. Conclusions: These findings extend the evidence that SEEG electrodes reflect the molecular microenvironments of brain activity in patients with epilepsy, both at sites of seizure onset and within the wider seizure network. The approach has potential applications in intraoperative surgical decision-making, as well as to identify molecular biomarkers or therapeutic targets for the drug-resistant epilepsies. Full article

(This article belongs to the Special Issue Molecular Biomarkers of Epileptogenesis)

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18 pages, 6780 KB

Open AccessEditor’s ChoiceArticle

Bile Acid Analogs with Anti-Germination Activities for Prophylaxis of Clostridioides difficile Infection Alter Bile Acid Homeostasis in the Enterohepatic Cycle

by Nivisa Vakeesan, Efren Heredia, Chandler Hassan, Yang Jiang, Shiv Sharma, Lianyong Su, Huiping Zhou, Steven Firestine, Ernesto Abel-Santos and Wanqing Liu

Biomolecules 2025, 15(12), 1672; https://doi.org/10.3390/biom15121672 - 1 Dec 2025

Viewed by 1085

Abstract

We previously reported that two bile acid (BA) analogs, CamSA and CA-Quin, demonstrate potent anti-germination activity against Clostridioides difficile (C. difficile) spores, protecting rodents from C. difficile infections. Here, we further evaluated the impact of these analogs on the hepatic transcriptome [...] Read more.

We previously reported that two bile acid (BA) analogs, CamSA and CA-Quin, demonstrate potent anti-germination activity against Clostridioides difficile (C. difficile) spores, protecting rodents from C. difficile infections. Here, we further evaluated the impact of these analogs on the hepatic transcriptome and BA homeostasis in vivo by focusing BA profiles on the liver, feces, and chyme as well as the hepatic transcriptome after a 7-day treatment. The two compounds demonstrated similar impact on BA profiles among the three samples, with significantly increased BA excretion in feces. This change is aligned with significantly altered expression of genes involved in BA homeostasis in both liver and gut tissues. Also, both compounds increased levels of deconjugated BAs in the feces, possibly suggesting increased activity of gut microbiota. Fecal levels of anti-C. difficile germination chenodeoxycholic acid and pro-germination taurocholic acid are significantly increased and decreased by the treatments, respectively. The hepatic transcriptome showed limited difference in gene expression between the three groups, suggesting a minimal adverse impact of the two compounds on liver function. Overall, our study suggests that in vivo CamSA and CA-Quin treatment demonstrated safe and significantly altered BA homeostasis that inhibits C. difficle germination. Full article

(This article belongs to the Special Issue Molecular Mechanisms and Therapeutic Strategies for Metabolic Dysfunction: From Molecules to Population Health)

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19 pages, 687 KB

Open AccessEditor’s ChoiceReview

Pharmacological and Pharmacokinetic Profile of Cannabidiol in Human Epilepsy: A Review of Metabolism, Therapeutic Drug Monitoring, and Interactions with Antiseizure Medications

by Ji-Hoon Na and Young-Mock Lee

Biomolecules 2025, 15(12), 1668; https://doi.org/10.3390/biom15121668 - 30 Nov 2025

Cited by 5 | Viewed by 2308

Abstract

Cannabidiol (CBD) has transitioned from anecdotal use to an evidence-based adjunctive therapy for Lennox–Gastaut syndrome, Dravet syndrome, and tuberous sclerosis complex. This review integrates knowledge on CBD’s pharmacology, pharmacokinetics, and clinical implementation, with focus on metabolism, therapeutic drug monitoring (TDM), and clinically relevant [...] Read more.

Cannabidiol (CBD) has transitioned from anecdotal use to an evidence-based adjunctive therapy for Lennox–Gastaut syndrome, Dravet syndrome, and tuberous sclerosis complex. This review integrates knowledge on CBD’s pharmacology, pharmacokinetics, and clinical implementation, with focus on metabolism, therapeutic drug monitoring (TDM), and clinically relevant interactions with antiseizure medications. CBD exerts CB1/CB2-independent mechanisms—prominently GPR55 antagonism, TRP-channel desensitization, and adenosine-mediated network dampening—supporting efficacy across heterogeneous seizure phenotypes. Its pharmacokinetic profile is characterized by low and variable oral bioavailability, a pronounced food effect, extensive tissue distribution, and phase I/II biotransformation to the active 7-hydroxy-CBD and abundant 7-carboxy-CBD, resulting in substantial inter-individual variability and liability for drug–drug interactions. Clinically salient interactions include CYP2C19-mediated elevation of N-desmethylclobazam and increased transaminases in valproate co-therapy. We summarize emerging TDM practices—standardized fed-state trough sampling with paired measurement of CBD and 7-hydroxy-CBD—and discuss how preliminary interpretive ranges can support dose optimization, adherence assessment, and safety surveillance. Practical recommendations emphasize interaction-aware titration within evidence-based dose bands, liver function monitoring, and standardized documentation of formulation and sampling conditions. Future work should align pharmacogenomics with TDM, refine bioavailability through advanced delivery systems, and tighten analytical and product-quality standards to consolidate CBD as a precision-ready component of modern epilepsy care. Full article

(This article belongs to the Section Molecular Medicine)

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14 pages, 1513 KB

Open AccessEditor’s ChoiceArticle

by Suzanne M. de la Monte, Ming Tong and Yiwen Yang

Biomolecules 2025, 15(12), 1670; https://doi.org/10.3390/biom15121670 - 30 Nov 2025

Cited by 1 | Viewed by 719

Abstract

Alcohol’s chronic neurotoxic and degenerative effects mediate alcohol-related brain damage (ARBD), which is marked by neurobehavioral, cognitive, and motor deficits. Major underlying abnormalities include impairments in signaling through the insulin and insulin-like growth factor (IGF) pathways, which regulate energy metabolism. This study examined [...] Read more.

Alcohol’s chronic neurotoxic and degenerative effects mediate alcohol-related brain damage (ARBD), which is marked by neurobehavioral, cognitive, and motor deficits. Major underlying abnormalities include impairments in signaling through the insulin and insulin-like growth factor (IGF) pathways, which regulate energy metabolism. This study examined the potential role of dysregulated incretin network-related mechanisms as mediators of ARBD and evaluated a non-invasive serum exosome (S-EV)-based approach for detecting brain abnormalities. Frontal lobe tissue and S-EVs isolated from Long–Evans adolescent rats maintained for 2 weeks on control or 24% ethanol (caloric) containing liquid diets (n = 8/group) were analyzed using multiplex magnetic bead-based enzyme-linked immunosorbent assays (ELISAs). ARBD was associated with significantly reduced insulin, C-peptide, glucagon, ghrelin, leptin, GIP, and amylin levels in the frontal lobe and/or S-EV samples. In contrast, chronic ethanol exposure had no significant effects on PP, PYY, or GLP-1, and it did not increase proinflammatory cytokine expression. Chronic ethanol feeding broadly affected (primarily inhibiting) the expression of metabolic hormones linked to insulin/IGF signaling. The reductions in GIP and amylin suggest potential targets for therapeutic intervention to enhance brain energy metabolism via insulin networks. On the other hand, the findings suggest that GLP-1 receptor agonists may have limited efficacy in remediating the effects of ARBD. Finally, the results support the use of non-invasive S-EV assays to detect and guide treatment for metabolic brain dysfunction in ARBD. Full article

(This article belongs to the Special Issue Alcohol-Related Nervous System Damage and Disease: From Mechanisms to Therapies)

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20 pages, 1200 KB

Open AccessEditor’s ChoiceReview

Arteriovenous Malformations (AVMs): Molecular Pathogenesis, Clinical Features, and Emerging Therapeutic Strategies

by Nga Le, Yan Li, Gianni Walker, Bao-Ngoc Nguyen, Arash Bornak, Sapna K. Deo, Omaida C. Velazquez and Zhao-Jun Liu

Biomolecules 2025, 15(12), 1661; https://doi.org/10.3390/biom15121661 - 27 Nov 2025

Cited by 3 | Viewed by 3691

Abstract

Arteriovenous malformations (AVMs) are fast-flow vascular malformations formed by direct artery-to-vein shunts without an intervening capillary bed, which increases the risk of hemorrhage and organ-specific damage. A synthesis of recent advances shows that AVMs arise from interplay between germline susceptibility (ENG, [...] Read more.

Arteriovenous malformations (AVMs) are fast-flow vascular malformations formed by direct artery-to-vein shunts without an intervening capillary bed, which increases the risk of hemorrhage and organ-specific damage. A synthesis of recent advances shows that AVMs arise from interplay between germline susceptibility (ENG, ACVRL1, SMAD4, RASA1, EPHB4), somatic mosaicism (KRAS, MAP2K1, PIK3CA), perturbed signaling (TGF-β/BMP, Notch, VEGF, PI3K/AKT, RAS/MAPK), hemodynamic stress, and inflammation. Multimodal imaging—digital subtraction angiography (DSA), MRI/MRA with perfusion and susceptibility sequences, CTA, Doppler ultrasound, and 3D rotational angiography—underpins diagnosis and risk stratification, while arterial spin labeling and 4D flow techniques refine hemodynamic assessment. Management is individualized and multidisciplinary, combining endovascular embolization, microsurgical resection, and stereotactic radiosurgery (SRS); a non-surgical approach and monitoring remain reasonable for some asymptomatic AVMs. Device and technique innovations (detachable-tip microcatheters, pressure-cooker approaches, and newer liquid embolics such as PHIL and Squid) have broadened candidacy, and precision-medicine strategies, including pathway-targeted pharmacotherapy, are emerging for syndromic and somatic-mutation–driven AVMs. Animal models and computational/radiomics tools increasingly guide hypothesis generation and treatment selection. We outline practical updates and future priorities: integrated genomic-imaging risk scores, genotype-informed medical therapy, rational hybrid sequencing, and long-term outcome standards focused on hemorrhage prevention and quality of life. Full article

(This article belongs to the Section Molecular Medicine)

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16 pages, 5177 KB

Open AccessEditor’s ChoiceArticle

Combinatorial Antimicrobial Effects of Imidazolium-Based Ionic Liquids and Antifungals on Model Fungal Organisms

by Jesus G. Calixto, Peter R. Fetz, Daniel Ammerman, Yesenia R. Flores, Gregory A. Caputo, Timothy D. Vaden and Benjamin R. Carone

Biomolecules 2025, 15(12), 1657; https://doi.org/10.3390/biom15121657 - 27 Nov 2025

Viewed by 2283

Abstract

Ionic Liquids (IL) are a unique class of molten salts, with specific formulations exhibiting antimicrobial properties. Several recent studies have highlighted the ability of ILs to form micelles, permeabilize the plasma membrane, and destabilize cellular structure, ultimately initiating cell death. Moreover, while these [...] Read more.

Ionic Liquids (IL) are a unique class of molten salts, with specific formulations exhibiting antimicrobial properties. Several recent studies have highlighted the ability of ILs to form micelles, permeabilize the plasma membrane, and destabilize cellular structure, ultimately initiating cell death. Moreover, while these membrane-destabilizing properties are cytotoxic to most cellular organisms at high concentrations, their membrane destabilization capability at lower concentrations may lead to improvements in drug delivery for combinatorial therapies against specific microbes. Work presented in this study aimed to identify a synergistic relationship between ILs, 1-n-Hexyl-3-methylimidazolium chloride (HMIM[Cl]) and 1-Methyl-3-n-octylimidazolium chloride (OMIM[Cl]), and antifungal drugs (AF), Clotrimazole, Ketoconazole, Fluconazole, and Itraconazole, with the hypothesis that in a combinatory setting there should be improved AF efficacy against model fungal organisms: S. boulardii, S. cerevisiae, S. pombe, and C. albicans. Several complementary assays were used to identify the combined effects of IL + AF treatment, including Kirby–Bauer tests and minimum inhibitory concentrations (MIC) assays to establish antimicrobial effects, and flow cytometry to evaluate cell wall permeability. Finally, we demonstrate that at low concentrations, the ILs tested in this study are capable of improving the effectiveness of current antifungal compounds at concentrations not cytotoxic to human cells. Full article

(This article belongs to the Section Molecular Medicine)

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25 pages, 1393 KB

Open AccessEditor’s ChoiceArticle

Plasma Membrane Lipid Composition and Turnover in Human Midbrain Neurons Investigated by Time-of-Flight Mass Spectrometry

by Emmanuel Berlin, Alicia A. Lork, Carl Ernst, John S. Fletcher and Nhu T. N. Phan

Biomolecules 2025, 15(12), 1650; https://doi.org/10.3390/biom15121650 - 24 Nov 2025

Cited by 1 | Viewed by 1802

Abstract

The molecular structure and dynamics of the neuronal plasma membrane are essential for neuronal biology and function. We employed time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging to investigate the lipid composition and turnover at the plasma membrane of single human midbrain neurons. The [...] Read more.

The molecular structure and dynamics of the neuronal plasma membrane are essential for neuronal biology and function. We employed time-of-flight secondary ion mass spectrometry (ToF-SIMS) imaging to investigate the lipid composition and turnover at the plasma membrane of single human midbrain neurons. The results showed that the profile of lipid turnover was heavily influenced by the types of precursors incorporated into the membrane lipids. In addition, there was a high prevalence of phosphatidylcholines, phosphatidylserines, and ceramides in the human midbrain neurons, and a preference for incorporating stearic acid into membrane lipids compared to other precursors. These features indicate a direct link between the membrane lipids to the biological state and functions of midbrain neurons. This is among a very few studies using mass spectrometry imaging to provide an insight into the native membrane lipid organization and lipid turnover using various lipid precursors in human neurons at a single cell level, illustrating their biological relevance in neuronal functions. Full article

(This article belongs to the Special Issue Mass Spectrometry Imaging in Neuroscience)

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16 pages, 1248 KB

Open AccessEditor’s ChoiceArticle

The Possible Role of Neurofilament Light Chain as a Serum Biomarker in Anorexia Nervosa: Clinical Implications

by Andrea Amerio, Eleonora Martino, Antonella Strangio, Andrea Aguglia, Benedetta Conio, Samir Giuseppe Sukkar and Daniele Saverino

Biomolecules 2025, 15(12), 1644; https://doi.org/10.3390/biom15121644 - 22 Nov 2025

Cited by 1 | Viewed by 1141

Abstract

Background: Neurofilament light chain (NfL) is a well-established biomarker of neuroaxonal damage, detectable in serum through immunoassays. Its potential relevance in psychiatric conditions, including anorexia nervosa (AN), is currently under investigation. This study aims to quantify serum NfL levels in individuals with AN, [...] Read more.

Background: Neurofilament light chain (NfL) is a well-established biomarker of neuroaxonal damage, detectable in serum through immunoassays. Its potential relevance in psychiatric conditions, including anorexia nervosa (AN), is currently under investigation. This study aims to quantify serum NfL levels in individuals with AN, evaluate their correlation with autoantibodies detection, and critically examine the specificity of NfL as a biomarker in this context. Methods: A total of 100 participants were enrolled, comprising 50 individuals diagnosed with AN and 50 age-matched, normal-weight controls. Serum concentrations of NfL and immunoglobulin G (IgG) antibodies reactive to hypothalamic antigens were measured using validated immunoassay techniques. Results: Serum NfL concentrations were markedly higher in the AN group compared to healthy controls. Interestingly, NfL levels tended to decrease with longer disease duration and with the recovery of body mass index (BMI), indicating a possible association between clinical improvement and reduced neuroaxonal damage. Furthermore, the results confirmed the presence of anti-hypothalamic autoantibodies and revealed a positive correlation between their levels and serum NfL concentrations. Conclusions: Clinical remission in AN appears to be linked to a decrease in both markers neuronal damage and hypothalamic autoimmunity. However, as elevated serum NfL is observed across a spectrum of neurological and psychiatric disorders, its specificity as a biomarker for AN should be further investigated. While NfL may reflect neuroaxonal injury in AN, its interpretation should be contextualized within a broader clinical and immunological framework. Full article

(This article belongs to the Special Issue Molecular Mechanisms and Signaling Pathways in Autoimmune Diseases)

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26 pages, 6015 KB

Open AccessEditor’s ChoiceArticle

Definition and Discovery of Tandem SH3-Binding Motifs Interacting with Members of the p47^phox-Related Protein Family

by Zsofia E. Kalman, Tamas Lazar, Laszlo Dobson and Rita Pancsa

Biomolecules 2025, 15(12), 1641; https://doi.org/10.3390/biom15121641 - 22 Nov 2025

Viewed by 1242

Abstract

SH3 domains are widespread protein modules that mostly bind to proline-rich short linear motifs (SLiMs). Most known SH3 domain-motif interactions and canonical or non-canonical recognition specificities are described for individual SH3 domains. Although cooperation and coordinated motif binding between tandem SH3 domains has [...] Read more.

SH3 domains are widespread protein modules that mostly bind to proline-rich short linear motifs (SLiMs). Most known SH3 domain-motif interactions and canonical or non-canonical recognition specificities are described for individual SH3 domains. Although cooperation and coordinated motif binding between tandem SH3 domains has already been described for members of the p47^phox-related protein family, individual cases have never been collected and analyzed collectively, which precluded the definition of the binding preferences and targeted discovery of further instances. Here, we apply an integrative approach that includes data collection, curation, bioinformatics analyses and state-of-the-art structure prediction methods to fill these gaps. A search of the human proteome with the sequence signatures of SH3 tandemization and follow-up structure analyses suggest that SH3 tandemization could be specific for this family. We define the optimal binding preference of tandemly arranged SH3 domains as [PAVIL]PPR[PR][^DE][^DE] and propose potential new instances of this SLiM among the family members and their binding partners. Structure predictions suggest the possibility of a novel, reverse binding mode for certain motif instances. In all, our comprehensive analysis of this unique SH3 binding mode enabled the identification of novel, interesting tandem SH3-binding motif candidates with potential therapeutic relevance. Full article

(This article belongs to the Special Issue Protein Biophysics)

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25 pages, 4434 KB

Open AccessEditor’s ChoiceArticle

Human Mutant Dynactin Subunit 1 Causes Profound Motor Neuron Disease Consistent with Possible Mechanisms Involving Axonopathy, Mitochondriopathy, Protein Nitration, and T-Cell-Mediated Cytolysis

by Victor Xie, Maria Clara Franco and Lee J. Martin

Biomolecules 2025, 15(12), 1637; https://doi.org/10.3390/biom15121637 - 21 Nov 2025

Viewed by 1414

Abstract

Mutations in the gene encoding the p150 subunit of the dynactin complex (DCTN1) are linked to amyotrophic lateral sclerosis, spinal and bulbar muscular atrophy, and Perry syndrome. These neurodegenerative diseases can cause muscle weakness and atrophy, parkinsonian-like symptoms, and paralysis. To [...] Read more.

Mutations in the gene encoding the p150 subunit of the dynactin complex (DCTN1) are linked to amyotrophic lateral sclerosis, spinal and bulbar muscular atrophy, and Perry syndrome. These neurodegenerative diseases can cause muscle weakness and atrophy, parkinsonian-like symptoms, and paralysis. To examine the evolution of neuropathology caused by a mutation in DCTN1 and cellular mechanisms of disease for therapeutic discovery, we characterized mice expressing either human wildtype or mutant (G59S) DCTN1. Neuron-specific expression of mutant, but not wildtype, DCTN1 caused fatal age-related paralytic disease and motor neuron (MN) degeneration in the spinal cord with axonopathy and chromatolysis without apoptotic morphology. MNs became positive for cleaved caspase-3, cleaved caspase-8, and nitrated Hsp90. Mitochondria accumulated and appeared fragmented and dysmorphic and then were lost. This pathology was accompanied by invasion of CD95- and CD8-positive mononuclear T cells into the ventral horn and accumulation of TNFα and IL9. Administration of the mitochondrial division inhibitor-1 (Mdivi-1) protected MNs and extended the lifespan of G59S-DCTN1 mice. A mitochondrial permeability transition pore inhibitor also extended lifespan. Thus, mutant DCTN1 causes degeneration of MNs associated with axonopathy, mitochondriopathy, nitrative stress, and caspase activation. It appears as retrograde neurodegeneration and inflammatory T-cell-like cytolysis. Mitochondria are possible therapeutic targets in DCTN1-linked neurodegenerative disorders. Full article

(This article belongs to the Special Issue Mitochondria and Central Nervous System Disorders: 3rd Edition)

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44 pages, 3780 KB

Open AccessEditor’s ChoiceReview

Lactobacilli-Derived Microbe-Associated Molecular Patterns (MAMPs) in Host Immune Modulation

by Salvatore Furnari, Ruben Ciantia, Adriana Garozzo, Pio Maria Furneri and Virginia Fuochi

Biomolecules 2025, 15(11), 1609; https://doi.org/10.3390/biom15111609 - 17 Nov 2025

Cited by 11 | Viewed by 3013

Abstract

Although traditionally sidelined by live probiotic effects, Lactobacilli-derived Microbe-Associated Molecular Patterns (MAMPs) are emerging as potent modulators of innate and adaptive immune responses, capable of acting independently of bacterial viability. However, the underlying mechanisms remain incompletely understood. These MAMPs, such as peptidoglycan (PGN), [...] Read more.

Although traditionally sidelined by live probiotic effects, Lactobacilli-derived Microbe-Associated Molecular Patterns (MAMPs) are emerging as potent modulators of innate and adaptive immune responses, capable of acting independently of bacterial viability. However, the underlying mechanisms remain incompletely understood. These MAMPs, such as peptidoglycan (PGN), lipoteichoic acid (LTA), and exopolysaccharides (EPSs), interact with pattern recognition receptors (PRRs) like Toll-like receptors (TLRs), initiating immune-signaling cascades that regulate cytokine production and inflammation. Lactobacilli-derived MAMPs exhibit dual immunomodulatory effects: they can enhance pro-inflammatory responses, e.g., interleukin-1β (IL-1β), IL-6, and tumor necrosis factor alpha (TNF-α) under inflammatory contexts, while enhancing regulatory pathways via IL-10 and regulatory T-cell (T_regs) induction in anti-inflammatory settings. Importantly, these immunomodulatory properties persist in the absence of bacterial viability, making MAMPs promising candidates for postbiotic therapies. This opens new avenues for MAMP-based strategies to target inflammation, overcoming the risks associated with live bacterial administration. This review examines the therapeutic relevance of non-viable MAMPs, particularly in inflammatory diseases where they have demonstrated benefits in reducing tissue damage, enhancing gut barrier function, and alleviating disease symptoms. Additionally, we discuss regulatory and translational challenges hindering their clinical implementation, highlighting the need for standardized characterization, a clear safety framework, and strain-specific profiling. Given their ability to fine-tune immune responses, MAMPs represent an emerging strategy for innovative treatments aimed at restoring immune balance and reinforcing host–microbe interactions. Full article

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

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18 pages, 7696 KB

Open AccessEditor’s ChoiceArticle

Interactive Role of the DHPR β_1a SH3 Domain in Skeletal Muscle Excitation–Contraction Coupling

by Yamuna Karunasekara, Shouvik Aditya, Nicole C. Norris, Jean Cappello, Angela F. Dulhunty, Philip G. Board, Jose M. Eltit, Claudio F. Perez and Marco G. Casarotto

Biomolecules 2025, 15(11), 1610; https://doi.org/10.3390/biom15111610 - 17 Nov 2025

Cited by 1 | Viewed by 1689

Abstract

Excitation–contraction (EC) coupling in skeletal muscle requires a physical interaction between the voltage-gated calcium channel, dihydropyridine receptor (DHPR), and the ryanodine receptor (RyR1) Ca²⁺ release channel. Although the exact mode of communication that links these two membrane proteins remains to be fully [...] Read more.

Excitation–contraction (EC) coupling in skeletal muscle requires a physical interaction between the voltage-gated calcium channel, dihydropyridine receptor (DHPR), and the ryanodine receptor (RyR1) Ca²⁺ release channel. Although the exact mode of communication that links these two membrane proteins remains to be fully resolved, both the α_1s and β_1a subunits of DHPR are two of a select number of critical proteins involved in this process. A detailed in vitro interaction study of these two proteins reveals that their association occurs between the β_1a SH3 domain and the polyproline motifs located in a critical region of the α_1s II-III loop. We demonstrate that subtle changes in the composition of the β_1a SH3 domain influences the ability of β proteins to bind to II-III loop proteins and investigate the effect of these changes on EC skeletal coupling. Furthermore, investigation into the composition of the II-III loop shows that previously identified amino acids demonstrated to be important in EC coupling are implicated in in vitro binding. In summary, we ascribe a role for the DHPR β_1a which involves the engagement of its SH3 domain with the α_1s II-III loop and propose a scenario whereby this interaction may facilitate skeletal muscle EC coupling. Full article

(This article belongs to the Special Issue The Role of Calcium Signaling in Cardiac and Skeletal Muscle)

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17 pages, 609 KB

Open AccessEditor’s ChoiceReview

RhoA/Rho-Kinase Signaling in Vascular Smooth Muscle and Endothelium: Mechanistic Insights and Translational Implications in Hypertension

by Stephanie Randar, Diana L. Silva-Velasco, Fernanda Priviero and R. Clinton Webb

Biomolecules 2025, 15(11), 1607; https://doi.org/10.3390/biom15111607 - 16 Nov 2025

Cited by 6 | Viewed by 2974

Abstract

The small GTPase RhoA and its downstream effector Rho-kinase (ROCK) have emerged as pivotal regulators of vascular smooth muscle cell (VSMC) contraction, endothelial function, and vascular remodeling. Activation of the RhoA/ROCK pathway enhances calcium (Ca²⁺) sensitivity by inhibiting myosin light chain [...] Read more.

The small GTPase RhoA and its downstream effector Rho-kinase (ROCK) have emerged as pivotal regulators of vascular smooth muscle cell (VSMC) contraction, endothelial function, and vascular remodeling. Activation of the RhoA/ROCK pathway enhances calcium (Ca²⁺) sensitivity by inhibiting myosin light chain phosphatase (MLCP), thereby promoting sustained vascular tone independent of intracellular Ca²⁺ levels. In endothelial cells (ECs), RhoA/ROCK signaling contributes to nitric oxide (NO) dysregulation, oxidative stress, cytoskeletal reorganization, and inflammatory activation. Cumulative evidence implicates this pathway in the development and progression of hypertension and other cardiovascular diseases, where maladaptive vascular remodeling, VSMC proliferation, and endothelial dysfunction drive increased vascular resistance. Translational studies have identified ROCK inhibitors and indirect modulators such as statins as promising therapeutic strategies. This review integrates recent mechanistic insights into RhoA/ROCK regulation of vascular function with clinical and translational perspectives on targeting this pathway in hypertension. Full article

(This article belongs to the Special Issue Calcium Signaling and Transport in Health and Disease: Recent Developments and New Insights)

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20 pages, 3608 KB

Open AccessEditor’s ChoiceArticle

Toll-like Receptor 7 Deficiency Attenuates Platelet Dysfunction in Sepsis

by Rashida Mohamed-Hinds, Arijit Dutta, Chanhee Park, Xiaomei Yang, Lin Zou, Wei Chao and Brittney Williams

Biomolecules 2025, 15(11), 1604; https://doi.org/10.3390/biom15111604 - 15 Nov 2025

Cited by 1 | Viewed by 1086

Abstract

Sepsis is a clinical syndrome caused by abnormal host response to infection. Thrombocytopenia and platelet dysfunction are common findings in sepsis and associated with worse outcomes. The innate immune single-stranded RNA sensor, Toll-like Receptor-7 (TLR7), plays a key role in thrombocytopenia in sepsis. [...] Read more.

Sepsis is a clinical syndrome caused by abnormal host response to infection. Thrombocytopenia and platelet dysfunction are common findings in sepsis and associated with worse outcomes. The innate immune single-stranded RNA sensor, Toll-like Receptor-7 (TLR7), plays a key role in thrombocytopenia in sepsis. This study investigated whether TLR7 signaling also contributes to platelet dysfunction in sepsis, and whether the bioactivity of downstream inflammatory mediators, specifically extracellular vesicles (EVs), is impacted by the TLR7 signaling pathway. Sepsis was induced in wild-type (WT) and TLR7-deficient (TLR7^−/−) mice by cecal ligation and puncture. Blood was collected at twenty-four hours for platelet and plasma isolation, and platelet function was assessed using aggregation, adhesion, and calcium flux assays. EVs were isolated from plasma and used in vitro to evaluate their impact on platelet–leukocyte aggregate (PLA) formation. We found that septic platelets are highly activated and more adhesive, yet show markedly impaired aggregation and reduced calcium signaling, indicating functional exhaustion despite activation. Notably, mice lacking TLR7 maintained stronger platelet aggregation, enhanced adhesion, and preserved calcium release in the septic state compared to wild-type controls, suggesting a protective effect of TLR7 deficiency. Plasma EVs increased in abundance and size during sepsis and promoted clot and PLA formation in vitro. Notably, EV-mediated platelet activation was reduced with EVs derived from TLR7-deficient mice. Our results demonstrate that while sepsis drives persistent platelet activation and dysfunction, TLR7 deficiency preserves platelet function and modulates the pathogenic activity of EV-mediated platelet activation, highlighting TLR7 as a key regulator and potential therapeutic target in sepsis-induced platelet dysfunction. Full article

(This article belongs to the Special Issue Innate Immunomodulation and Inflammation: From Molecular Mechanisms to Pre-Clinical Insights)

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14 pages, 814 KB

Open AccessEditor’s ChoiceArticle

Serum PTH ≥ 40 pg/mL as a Marker of Bone Fragility and Vitamin D Deficiency in Periodontitis Patients: Biochemical, Densitometric and Genetic Evidence

by Giada Marroncini, Serena Martinelli, Francesco Petrelli, Francesco Bombardiere, Antonio Sarnataro and Francesco Saverio Martelli

Biomolecules 2025, 15(11), 1600; https://doi.org/10.3390/biom15111600 - 14 Nov 2025

Cited by 1 | Viewed by 1208

Abstract

(1) Background: this study aimed to determine whether a serum parathyroid hormone (PTH) threshold of 40 pg/mL represents a clinically relevant risk factor for vitamin D (VitD) deficiency and reduced bone mineral density (BMD). It also investigated potential genetic interactions influencing PTH regulation [...] Read more.

(1) Background: this study aimed to determine whether a serum parathyroid hormone (PTH) threshold of 40 pg/mL represents a clinically relevant risk factor for vitamin D (VitD) deficiency and reduced bone mineral density (BMD). It also investigated potential genetic interactions influencing PTH regulation and skeletal health in patients with periodontitis. (2) Methods: a cross-sectional analysis was conducted on 1038 periodontitis patients (35–75 years). Serum PTH, VitD, calcium (Ca), phosphate (P), and urinary parameters were assessed. Dual-energy X-ray absorptiometry (DXA) was used to evaluate BMD in 261 subjects. Vitamin D Receptor (VDR) and estrogen receptor alpha (ERα) polymorphisms were genotyped, and composite genetic risk scores were calculated. Statistical analyses included correlation tests, subgroup comparisons, and regression models. (3) Results: sixty-two percent of individuals had PTH > 40 pg/mL, which was associated with significantly lower 25(OH)D and Ca levels and reduced T-scores (p < 0.05). PTH levels negatively correlated with BMD (Pearson’s r = –0.159, p = 0.0105). Patients with higher ERα polymorphism scores showed increased PTH values (p < 0.05), while VDR variants demonstrated a positive but no significant trend. (4) Conclusions: a PTH threshold of 40 pg/mL identifies individuals at higher risk of VitD deficiency and skeletal fragility, even without overt hypercalcemia. Genetic factors, particularly ERα variants, may contribute to elevated PTH levels, suggesting value in integrating biochemical, densitometric, and genetic screening for early bone health risk stratification. Full article

(This article belongs to the Special Issue Biomolecules and Materials Based Approaches in Biomedical Field: 2nd Edition)

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15 pages, 3999 KB

Open AccessEditor’s ChoiceArticle

Kisspeptin-10 Ameliorates Obesity-Diabetes with Diverse Effects on Ileal Enteroendocrine Cells and Pancreatic Islet Morphology in High-Fat Fed Female Mice

by Ananyaa Sridhar, Dawood Khan, Rithiga Muthukumar, Swetha Sampathkumar, Nigel Irwin, Peter R. Flatt and R. Charlotte Moffett

Biomolecules 2025, 15(11), 1591; https://doi.org/10.3390/biom15111591 - 13 Nov 2025

Viewed by 3075

Abstract

Kisspeptin is a neuropeptide recognised for a pivotal role within the reproductive system, but potentially important endocrine metabolic effects are less well understood. We examined effects of twice-daily intraperitoneal administration of saline vehicle or kisspeptin-10 (25 nmol/kg), for 21 days, on glucose homeostasis, [...] Read more.

Kisspeptin is a neuropeptide recognised for a pivotal role within the reproductive system, but potentially important endocrine metabolic effects are less well understood. We examined effects of twice-daily intraperitoneal administration of saline vehicle or kisspeptin-10 (25 nmol/kg), for 21 days, on glucose homeostasis, energy balance, circulating hormones as well as the morphology-function of enteroendocrine and islet cells in high-fat diet (HFD) fed female mice, with normal diet (ND) mice as an additional control group. Kisspeptin-10 decreased body weight, blood glucose and energy intake to ND levels. HFD increased circulating follicle-stimulating hormone (FSH) levels, which were further enhanced by kisspeptin-10 along with luteinising hormone (LH) concentrations. Neither HFD nor kisspeptin-10 affected progesterone or corticosterone. In the ileum, kisspeptin-10 decreased crypt depth and restored villi length to ND control levels, as well as increasing the proportion of glucose-dependent insulinotropic polypeptide (GIP) positive cells when compared to HFD mice and glucagon-like peptide-1 (GLP-1) positive cells compared to ND mice. Peptide YY (PYY) immunoreactivity was unaltered by HFD or kisspeptin-10. Plasma GIP was unchanged but circulating GLP-1 and PYY were reduced to ND levels. Within the pancreas, total islet, beta- and alpha-cell areas were similar in all mice, but kisspeptin-10 intervention restored relative insulin area to ND levels. Glucagon radius, an indicator of peripherally located alpha-cells, was reduced in HFD mice but normalised by kisspeptin-10 alongside elevated glucagon-islet area. Notably, beta-cell proliferation was increased by kisspeptin-10 with no alteration in beta-cell apoptosis. Overall, we reveal a previously uncharacterised diverse metabolic role for kisspeptin in directly modulating the gut–pancreatic axis. Full article

(This article belongs to the Special Issue Metabolic Inflammation and Insulin Resistance in Obesity)

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13 pages, 1729 KB

Open AccessEditor’s ChoiceArticle

Ecological History Shapes Transcriptome Variation in Quiescent Saccharomyces cerevisiae

by Agnieszka Marek, Katarzyna Tomala and Dominika Wloch-Salamon

Biomolecules 2025, 15(11), 1588; https://doi.org/10.3390/biom15111588 - 12 Nov 2025

Cited by 1 | Viewed by 735

Abstract

Quiescence is a pivotal state for all living organisms and cells. However, recent research indicates a lack of uniformity among quiescent cells. That is, even if the primary feature of quiescence—the ability to restart divisions—is maintained, quiescent cells within populations exhibit variation in [...] Read more.

Quiescence is a pivotal state for all living organisms and cells. However, recent research indicates a lack of uniformity among quiescent cells. That is, even if the primary feature of quiescence—the ability to restart divisions—is maintained, quiescent cells within populations exhibit variation in their cellular architecture and characteristics. While it is known that the process of entry into quiescence is influenced by a combination of nutrient starvation and temporal factors, the underlying mechanisms remain to be fully elucidated. In this study, we compare the transcriptomes of known homogenous fractions of dense quiescent yeast isolated from populations of different ecological histories. These populations have undergone experimental enrichment of certain types of quiescent cells during cycles of growth and starvation for 300 generations. Transcriptome analysis revealed discrepancies in terms of characteristics associated mainly with energy turnover processes, biosynthesis, and cell wall maintenance. The results of this study suggest that quiescent cells possess the capacity to adapt their transcriptome activity in accordance with their evolutionary history. Full article

(This article belongs to the Special Issue Cellular Quiescence and Dormancy)

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43 pages, 1639 KB

Open AccessEditor’s ChoiceReview

The Type I Interferon Axis in Systemic Autoimmune Diseases: From Molecular Pathways to Targeted Therapy

by Ryuhei Ishihara, Ryu Watanabe, Mayu Shiomi, Yuya Fujita, Masao Katsushima, Kazuo Fukumoto, Shinsuke Yamada and Motomu Hashimoto

Biomolecules 2025, 15(11), 1586; https://doi.org/10.3390/biom15111586 - 12 Nov 2025

Cited by 8 | Viewed by 5820

Abstract

Type I interferons (IFN-I) are pivotal effectors of innate immunity and constitute a central axis of host defense against pathogens. Sensing of exogenous or endogenous nucleic acids by pattern-recognition receptors—exemplified by Toll-like receptors—triggers transcriptional induction of IFN-I. Engagement of the heterodimeric IFN-I receptor [...] Read more.

Type I interferons (IFN-I) are pivotal effectors of innate immunity and constitute a central axis of host defense against pathogens. Sensing of exogenous or endogenous nucleic acids by pattern-recognition receptors—exemplified by Toll-like receptors—triggers transcriptional induction of IFN-I. Engagement of the heterodimeric IFN-I receptor on nucleated cells reprograms cellular states via canonical Janus kinase–signal transducer and activator of transcription (JAK–STAT) signaling as well as STAT-independent, noncanonical pathways. This axis is tempered by multilayered regulatory mechanisms, including epigenetic remodeling, and important aspects remain incompletely defined. Dysregulation of IFN-I activity underlies diverse autoimmune disorders, notably systemic lupus erythematosus, wherein IFN-responsive gene signatures stratify disease endotypes, reflect disease activity trajectories, and predict therapeutic responsiveness. In recent years, therapeutic strategies targeting this pathway are now available: anti-IFN-I receptor therapy for systemic lupus erythematosus (SLE) and JAK inhibition for rheumatoid arthritis (RA) and giant cell arteritis (GCA). Altogether, a refined understanding of the IFN-I axis furnishes a pragmatic framework for patient stratification, response prediction, and mechanism-informed therapy design across immune-mediated diseases. Full article

(This article belongs to the Section Biological Factors)

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17 pages, 2837 KB

Open AccessEditor’s ChoiceArticle

Comprehensive Analysis of the Putative Substratome of FAM20C, the Master Serine Kinase of the Secretory Pathway

by Luca Cesaro, Francesca Noventa, Trinidad De Los Angeles Cordero, Barbara Molon, Valentina Bosello Travain, Maria Cristina Aspromonte and Mauro Salvi

Biomolecules 2025, 15(11), 1582; https://doi.org/10.3390/biom15111582 - 11 Nov 2025

Cited by 1 | Viewed by 1308

Abstract

FAM20C, previously known as Golgi casein kinase (GCK), is a serine/threonine kinase localized to the Golgi apparatus and classified within the acidophilic kinase family. Its phosphorylation motif is characterized by a glutamic acid residue at the +2 position relative to the target site. [...] Read more.

FAM20C, previously known as Golgi casein kinase (GCK), is a serine/threonine kinase localized to the Golgi apparatus and classified within the acidophilic kinase family. Its phosphorylation motif is characterized by a glutamic acid residue at the +2 position relative to the target site. Before its molecular identity was established, analysis of a limited number of phosphosites in secreted proteins showed that around 70% matched the GCK consensus sequence, suggesting that GCK is the principal kinase for secreted proteins. Following the identification of GCK as FAM20C, the generation of FAM20C knockout cell lines and phosphoproteomic data confirmed its role: approximately 80% of serine/threonine phosphosites in the secretome of two different human cell lines were shown to depend on FAM20C. In this study, comparative analysis of in vitro phosphorylation datasets from a broad panel of recombinant Ser/Thr kinases confirmed that the FAM20C consensus sequence is distinct from those of other acidophilic kinases. Examination of experimentally identified human phosphosites within the secretory pathway revealed strong conservation of the FAM20C consensus, firmly establishing this enzyme as the master Ser kinase of the entire pathway. From this dataset, we defined the putative FAM20C substratome, comprising 443 phosphosites across 256 proteins, ~77% of which had not been previously linked to FAM20C. This represents the most extensive FAM20C substratome to date and a valuable resource for functional studies. Notably, enrichment analysis highlights strong links between FAM20C and major extracellular pathways, including collagen fibril organization, complement activation, and blood coagulation, underscoring an underappreciated role for this kinase in regulating hemostasis and innate immunity. Full article

(This article belongs to the Special Issue Feature Papers in Cellular Biochemistry)

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19 pages, 3546 KB

Open AccessEditor’s ChoiceArticle

Molecular Dynamics Study of α-Synuclein Domain Deletion Mutant Monomers

by Noriyo Onishi, Nicodemo Mazzaferro, Špela Kunstelj, Daisy A. Alvarado, Anna M. Muller and Frank X. Vázquez

Biomolecules 2025, 15(11), 1577; https://doi.org/10.3390/biom15111577 - 10 Nov 2025

Cited by 1 | Viewed by 1112

Abstract

Aggregates of misfolded α-synuclein proteins are key markers of Parkinson’s disease. The protein α-synuclein (aSyn) is an intrinsically disordered protein (IDP) and therefore lacks a single stable 3D structure, instead sampling multiple conformations in solution. It is primarily located in presynaptic terminals and [...] Read more.

Aggregates of misfolded α-synuclein proteins are key markers of Parkinson’s disease. The protein α-synuclein (aSyn) is an intrinsically disordered protein (IDP) and therefore lacks a single stable 3D structure, instead sampling multiple conformations in solution. It is primarily located in presynaptic terminals and is thought to help regulate synaptic vesicle trafficking and neurotransmitter release. ASyn proteins have three domains: an N-terminal domain, a hydrophobic non-amyloid-β component (NAC) core implicated in aggregation, and a proline-rich C-terminal domain. Asyn proteins with truncated C-terminal domains are known to be prone to aggregation and suggest that understanding domain–domain interactions in aSyn monomers could help elucidate the role of the flanking domains in modulating protein structure. To this end, we used Gaussian accelerated molecular dynamics (GAMD) to simulate wild-type (WT), N-terminal truncated (ΔN), C-terminal truncated (ΔC), and isolated NAC domain (isoNAC) aSyn protein variants. Using clustering and contact analysis, we found that removal of the N-terminal domain led to increased contacts between NAC and C-terminal domains and the formation of inter-domain β-sheets. Removal of either flanking domain also resulted in increased compactness of every domain. We also found that the contacts between flanking domains in the WT protein result in an electrostatic potential (ESP) that may lead to favorable interactions with anionic lipid membranes. Removal of the C-terminal domain disrupts the ESP in a way that could result in over-stabilized protein–membrane interactions. These results suggest that cooperation between the flanking domains may modulate the protein’s structure in a way that helps maintain elongation and creates an ESP that may aid favorable interactions with the membrane. Full article

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

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20 pages, 11004 KB

Open AccessEditor’s ChoiceReview

Local Insulin for Local Needs? Insights into Retinal Insulin Signaling and RPE Metabolism

by Matilde Balbi, Alessandra Puddu, Andrea Amaroli, Davide Maggi, Isabella Panfoli and Silvia Ravera

Biomolecules 2025, 15(11), 1570; https://doi.org/10.3390/biom15111570 - 8 Nov 2025

Viewed by 3144

Abstract

Insulin is a key anabolic hormone traditionally considered to be exclusively produced by pancreatic β-cells. Insulin exerts several systemic effects involved in glucose uptake and metabolism. In the retina, insulin signaling acts as a regulator of photoreceptor- retinal pigment epithelium (RPE) metabolic coupling [...] Read more.

Insulin is a key anabolic hormone traditionally considered to be exclusively produced by pancreatic β-cells. Insulin exerts several systemic effects involved in glucose uptake and metabolism. In the retina, insulin signaling acts as a regulator of photoreceptor- retinal pigment epithelium (RPE) metabolic coupling as well as of neuronal survival via the PI3K/Akt and MAPK/ERK pathways. Impaired insulin signaling contributes to diabetic retinopathy, retinitis pigmentosa, and age-related degeneration by disrupting energy homeostasis and trophic support. However, growing evidence suggests that the retina, particularly RPE, locally synthesizes and secretes insulin. Although the role of local insulin production in the retina remains to be clarified, this discovery introduces a paradigm shift in retinal physiology, suggesting a self-sustaining insulin signaling system that supports glucose uptake, lipid metabolism, and neurovascular integrity. Emerging data indicate that RPE-derived insulin is stimulated by photoreceptor outer segment (POS) phagocytosis and may act through autocrine and paracrine mechanisms to maintain retinal function, even under conditions of systemic insulin deficiency. Understanding this extra-pancreatic insulin source opens new therapeutic perspectives aimed at enhancing local insulin signaling to preserve vision and prevent retinal degeneration. Thus, the objective of this review is to summarize current evidence on RPE-derived insulin and to discuss its potential implications for retinal homeostasis and disease. Full article

(This article belongs to the Special Issue State of the Art and Perspectives in Retinal Pigment Epithelium)

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25 pages, 1392 KB

Open AccessEditor’s ChoiceReview

Translational Molecular and Fluid Biomarkers for Age-Related Macular Degeneration: Practical Insights from Animal Models and Humans

by Simona Intonti, Chiara Olivieri, Michele Reibaldi, Enrico Borrelli, Claudia Curcio and Federica Maria Conedera

Biomolecules 2025, 15(11), 1571; https://doi.org/10.3390/biom15111571 - 8 Nov 2025

Cited by 1 | Viewed by 2268

Abstract

Age-related macular degeneration (AMD) is a leading cause of irreversible central vision loss. Its pathogenesis is complex and multifactorial, involving genetic predisposition, inflammation, oxidative stress, and environmental influences, which underscores the need to better understand biomarkers associated with the disease. This review provides [...] Read more.

Age-related macular degeneration (AMD) is a leading cause of irreversible central vision loss. Its pathogenesis is complex and multifactorial, involving genetic predisposition, inflammation, oxidative stress, and environmental influences, which underscores the need to better understand biomarkers associated with the disease. This review provides a comprehensive translational overview of biomarkers linked to both dry and wet forms of AMD by integrating findings from human studies and preclinical mouse models, including chemical, genetic, and laser-induced paradigms. It outlines key tissue, fluid, and systemic biomarkers related to oxidative stress, inflammation, complement activation, extracellular matrix remodeling, angiogenesis, and gut microbiota alterations. The main findings highlight similarities and differences between human AMD and animal models, identify challenges in biomarker validation, and emphasize the potential of combining biomarker profiles from ocular tissues, blood, tear fluid, aqueous and vitreous humor, and gut microbiome samples to improve early diagnosis, therapeutic monitoring, and personalized treatment strategies. These insights suggest that integrating experimental and clinical biomarker data could advance precision medicine in AMD, facilitating better early detection and individualized therapies. Future research should aim to bridge these datasets to optimize biomarker-driven approaches for AMD management. Full article

(This article belongs to the Section Molecular Biomarkers)

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