International Journal of Molecular Sciences

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Open AccessArticle

Proteomic Profiling of Limited-Stage Follicular Lymphoma Reveals Differentially Expressed Proteins Linked to Disease Progression Post-Radiation Therapy

by Jonas Klejs Hemmingsen, Marie Hairing Enemark, Emma Frasez Sørensen, Cecilie Dohrmann, Kristina Lystlund Lauridsen, Stephen Jacques Hamilton-Dutoit, Robert Kridel, Bent Honoré and Maja Ludvigsen

Int. J. Mol. Sci. 2025, 26(19), 9306; https://doi.org/10.3390/ijms26199306 - 23 Sep 2025

Abstract

Follicular lymphoma (FL) is the most common indolent lymphoma. Despite a generally favorable prognosis and long-term survival for many patients, FL remains incurable, with disease progression occurring in approximately half of limited-stage FL cases. In this study, we employed high-throughput mass spectrometry-based proteomics [...] Read more.

Follicular lymphoma (FL) is the most common indolent lymphoma. Despite a generally favorable prognosis and long-term survival for many patients, FL remains incurable, with disease progression occurring in approximately half of limited-stage FL cases. In this study, we employed high-throughput mass spectrometry-based proteomics to explore the differential protein expression in diagnostic lymphoma biopsies from 26 limited-stage FL patients. Of these, 9 patients experienced subsequent disease progression (sp-FL), while 17 did not (np-FL). A total of 1940 proteins were identified, with 78 showing significant differential expression between progressing and non-progressing cases. Unsupervised clustering analyses were able to separate the two patient groups based on these differential protein profiles. Notably, proteins involved in metabolism, immune regulation, and apoptosis were downregulated in sp-FL samples. Among the identified proteins, caspase 4 and 8 (CASP4 and CASP8) were further evaluated. The low expression of CASP4 in the diagnostic lymphoma tissue correlated with shorter progression-free survival (PFS) (p < 0.001), primarily with this difference apparent in the expression profiles in the intrafollicular areas (p = 0.015). Similarly, low CASP8 expression was associated with inferior PFS (p = 0.031). Interestingly, addressing the expression pattern for advanced-stage FL patients, the low protein expression of both CASP4 and CASP8 was also found to be associated with progressing cases, suggesting their potential role in disease pathogenesis independent of the disease stage. With further research, the expression pattern of CASP4 and CASP8 may enable the early prediction of disease progression in FL patients, which may ultimately improve patient stratification and allow for more individualized treatment strategies. Full article

(This article belongs to the Special Issue Role of Proteomics in Human Diseases and Infections)

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Open AccessArticle

Intra-Articular Administration of Recombinant Human Proteoglycan 4 (rhPRG4) as a Potential Therapy for Temporomandibular Joint Osteoarthritis: A Preclinical Histopathological Study

by Veronica Iturriaga, Bélgica Vásquez, Schilin Wen, Thomas Bornhardt, Javiera Navarrete and Mariano del Sol

Int. J. Mol. Sci. 2025, 26(19), 9305; https://doi.org/10.3390/ijms26199305 - 23 Sep 2025

Abstract

The proposed research aims to evaluate the histopathological effects of the intra-articular administration of recombinant human proteoglycan 4 (rhPRG4) on an experimental model of induced temporomandibular joint (TMJ) osteoarthritis (OA) in rabbits. An experimental study was conducted on rabbit TMJs. Twenty-four TMJs were [...] Read more.

The proposed research aims to evaluate the histopathological effects of the intra-articular administration of recombinant human proteoglycan 4 (rhPRG4) on an experimental model of induced temporomandibular joint (TMJ) osteoarthritis (OA) in rabbits. An experimental study was conducted on rabbit TMJs. Twenty-four TMJs were included, distributed as follows: (1) TMJ-C, a control group consisting of four healthy TMJs; (2) TMJ-OA, a group consisting of five TMJs with OA; (3) TMJ-OA-WT, a group consisting of five untreated TMJ-OAs; (4) rhPRG4-30, a group consisting of five TMJ-OAs treated with rhPRG4 30 μg/mL; and (5) rhPRG4-100, a group consisting of five TMJ-OAs treated with rhPRG4 100 μg/mL. A histopathological analysis was performed, considering the mandibular condyle, articular disc, and mandibular fossa, comparing the groups. In addition, a quantitative comparative analysis was performed using the Osteoarthritis Research Society International (OARSI) scale. Kruskal–Wallis and Dunn’s post hoc tests were used for statistical analysis, considering a statistical significance of p < 0.05. The histological analysis of TMJ tissue reveals key differences between healthy, osteoarthritic, and rhPRG4-treated joints. The intra-articular infiltration of rhPRG4 in TMJ-OA has a cartilage and articular disc repair effect, reducing the severity of osteoarthritis and promoting a more organized cartilage structure, with slightly better results at the 30 μg/mL concentration. Full article

(This article belongs to the Special Issue Recent Advances in Osteoarthritis Pathways and Biomarker Research)

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Open AccessArticle

Genome-Wide Characterization of a Carbon Ion Beam-Induced Soybean Mutant Population Reveals Extensive Genetic Variation for Trait Improvement

by Xiulin Liu, Kezhen Zhao, Xueyang Wang, Chunlei Zhang, Fengyi Zhang, Rongqiang Yuan, Sobhi F. Lamlom, Bixian Zhang and Honglei Ren

Int. J. Mol. Sci. 2025, 26(19), 9304; https://doi.org/10.3390/ijms26199304 - 23 Sep 2025

Abstract

Understanding the genetic architecture of complex traits is crucial for crop improvement and molecular breeding. We developed a mutagenized soybean population using carbon ion beam irradiation and conducted genome-wide association studies (GWAS) to identify variants controlling key agronomic traits. Whole-genome resequencing of 199 [...] Read more.

Understanding the genetic architecture of complex traits is crucial for crop improvement and molecular breeding. We developed a mutagenized soybean population using carbon ion beam irradiation and conducted genome-wide association studies (GWAS) to identify variants controlling key agronomic traits. Whole-genome resequencing of 199 M4 lines revealed 1.48 million SNPs, predominantly C→T transitions, with population structure analysis identifying three distinct genetic groups. GWAS across five traits revealed striking differences in genetic architecture: the podding habit showed extreme polygenic control with 87,029 significant associations of small effect, while pubescence color exhibited oligogenic inheritance with only 122 variants. Hundred-seed weight displayed moderate complexity (4637 associations) with the largest effect sizes (−3.74 to 5.03) and major QTLs on chromosomes 4, 7, and 15–20. Growth habit involved 12,136 SNPs, including a strong chromosome 3 association (−log₁₀(p-value) > 50). Flower color showed 2662 associations clustered on chromosome 15. Functional analysis of 18,542 candidate genes revealed trait-specific pathway enrichments: flavonoid biosynthesis for flower color, phloem transport for seed weight, auxin signaling for growth habit, and amino acid transport for podding habit. This study demonstrates how mutagenesis-induced variation, combined with association mapping, reveals evolutionary constraints that shape genetic architectures, providing insights for genetics-assisted breeding strategies. Full article

(This article belongs to the Special Issue Functional and Structural Genomics Studies for Plant Breeding)

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Open AccessFeature PaperArticle

Phlorizin Ameliorates Amyloid-β Toxicity and Enhances Fatty Acid β-Oxidation in Caenorhabditis elegans via NHR-49-Dependent Pathway

by Xuya Zhang, Yan Fu, Xue Li, Yali Zhang, Lingling Li, Tianxing Yi, Hong Jiang and Yi Lu

Int. J. Mol. Sci. 2025, 26(19), 9303; https://doi.org/10.3390/ijms26199303 - 23 Sep 2025

Abstract

Phlorizin (PHZ) is a glucoside of phloretin, belonging to the dihydrochalcone class within flavonoids; It is one of the active ingredients of the plant Cynomorium, and it has been shown that PHZ can regulate lipid metabolism disorders as well as having anti-aging properties. [...] Read more.

Phlorizin (PHZ) is a glucoside of phloretin, belonging to the dihydrochalcone class within flavonoids; It is one of the active ingredients of the plant Cynomorium, and it has been shown that PHZ can regulate lipid metabolism disorders as well as having anti-aging properties. However, no studies have investigated whether PHZ ameliorates Aβ-induced toxicity in Alzheimer’s disease (AD) by regulating fatty acid β-oxidation. This study aims to investigate the effects of PHZ on the regulation of fatty acid β-oxidation and resistance to Aβ-associated toxicity on the AD Caenorhabditis elegans and the mechanisms of action. Wild-type N2 and AD model CL4176 C. elegans were used; lifespan, heat stress resistance, chronic paraquat stress, reactive oxygen species (ROS), behavioral performance, and lipofuscin accumulation assays were examined to evaluate the anti-aging effects; and non-esterified fatty acid (NEFA), triglyceride (TG) and lipidomic contents were quantified after PHZ treatment. The detection of genes related to fatty acid β-oxidation pathways was performed using qRT-PCR. nhr-49 knockout mutant RB1716; and GFP-binding mutants PMD150 WBM170 were used to observe the effect of PHZ on NHR-49 pathways, and molecular docking studies were performed by combining PHZ with NHR-49 proteins. Results showed that PHZ improved worms’ survival and delayed senescence, as demonstrated by enhanced performance in lifespan, heat stress, ROS, and paraquat assays and chronic paraquat assays; PHZ also reduced lipid accumulation in worms, affected the unsaturated fatty acid pathway, and significantly increased the expression of fatty acid metabolism-related genes nhr-49, acs-2, and cpt-5, and can be tightly coupled to NHR-49 targets. PHZ may play an anti-Aβ toxicity role by regulating lipid metabolism disorders through the NHR-49—related pathway and anti-aging in AD worms. Full article

(This article belongs to the Special Issue Characterization and Biological Function of Plant Extracts)

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Open AccessCase Report

13q Deletion Syndrome Presenting with Lymphopenia Detected Through Newborn Screening for Primary Immunodeficiencies

by Irina Efimova, Anna Mukhina, Zhanna Markova, Sergey Mordanov, Irina Soprunova, Dmitry Pershin, Natalya Balinova, Yunna Petrusenko, Dmitry Meleshko, Rena Zinchenko, Nadezhda Shilova, Sergey Voronin, Anna Shcherbina, Sergey Kutsev and Andrey Marakhonov

Int. J. Mol. Sci. 2025, 26(19), 9302; https://doi.org/10.3390/ijms26199302 - 23 Sep 2025

Abstract

The expanded newborn screening (NBS) program in the Russian Federation, launched in 2023, includes the detection of severe forms of T- and B-cell immunodeficiencies via TREC/KREC quantification. We report a rare case of a male infant having multiple congenital anomalies and lymphopenia identified [...] Read more.

The expanded newborn screening (NBS) program in the Russian Federation, launched in 2023, includes the detection of severe forms of T- and B-cell immunodeficiencies via TREC/KREC quantification. We report a rare case of a male infant having multiple congenital anomalies and lymphopenia identified through this program. Genetic testing revealed a 25.8 Mb terminal deletion spanning 13q31.2–qter, consistent with 13q deletion syndrome. Initial NBS revealed reduced TREC levels, prompting further evaluation. The patient exhibited a complex phenotype, including central nervous system malformation (alobar holoprosencephaly), severe congenital heart disease, renal hypoplasia, limb and genitourinary anomalies, and facial dysmorphism. Postnatal complications included pneumonia, pleuritis, and chylothorax. Flow cytometry demonstrated mild T- and B-cell lymphopenia. The genomic defect was characterized using long-read third-generation sequencing, enabling precise breakpoint identification and accurate mapping of deleted genes. The deletion was confirmed via subtelomeric FISH analysis. The patient died at 7 months of age due to the progression of underlying congenital anomalies and associated complications. Our findings broaden the clinical characterization of distal 13q deletion syndrome and demonstrate the value of long-read sequencing in structural chromosomal analysis. They further highlight the difficulties of caring for neonates having complex malformations and immune dysfunction. Given the potential for both primary and secondary immune disturbances, comprehensive immunological evaluation should be considered in patients having 13q deletion syndrome to improve diagnostic accuracy and inform appropriate clinical management. Full article

(This article belongs to the Special Issue Genes and Human Diseases: 3rd Edition)

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Open AccessBrief Report

Lipid Signature of Motile Human Sperm: Characterization of Sphingomyelin, Ceramide, and Phospholipids with a Focus on Very Long Chain Polyunsaturated Fatty Acids

by Gerardo Martín Oresti, Jessica Mariela Luquez and Silvia Alejandra Belmonte

Int. J. Mol. Sci. 2025, 26(19), 9301; https://doi.org/10.3390/ijms26199301 - 23 Sep 2025

Abstract

Sperm membrane lipids play a crucial role in male fertility, influencing sperm motility, viability, and functional competence. This study comprehensively characterizes the phospholipid and sphingolipid composition in highly motile human spermatozoa obtained through the swim-up method, a widely used technique in assisted reproductive [...] Read more.

Sperm membrane lipids play a crucial role in male fertility, influencing sperm motility, viability, and functional competence. This study comprehensively characterizes the phospholipid and sphingolipid composition in highly motile human spermatozoa obtained through the swim-up method, a widely used technique in assisted reproductive technology (ART). Using two-dimensional thin-layer chromatography and phosphorus analysis, we identified choline glycerophospholipids (CGP, 45%), ethanolamine glycerophospholipids (EGP, 26%), and sphingomyelin (SM, 17%) as predominant phospholipids, with minor components including cardiolipin, lysophospholipids, phosphatidylinositol, phosphatidylserine, phosphatidic acid, and neutral lipids. Gas chromatography analysis of glycerophospholipids (GPL) revealed a high long chain (C20–C22) polyunsaturated fatty acids (PUFA) content (46.3%), particularly docosahexaenoic acid (DHA, 22:6n-3), which was more abundant in CGP (46%) than EGP (26%). Sphingolipid analysis indicated that ceramide (Cer) and SM shared similar fatty acid profiles due to their metabolic relationship, with very-long-chain (VLC) PUFA (≥C26) being more prevalent in SM (10%) than in Cer (6%). Additionally, argentation chromatography identified highly unsaturated VLCPUFA species in Cer, including 28:3n-6, 28:4n-6, and 30:4n-6, which had not been previously quantified in motile human spermatozoa. Given the essential function of sphingolipid metabolism in spermatogenesis, capacitation, and acrosomal exocytosis, our findings suggest that the balance of VLCPUFA-containing SM and Cer could play a role in sperm performance and fertilization potential. This study provides novel insights into the lipid signature of human sperm and highlights the relevance of membrane lipid remodeling for male fertility and ART outcomes. Full article

(This article belongs to the Special Issue Sphingolipid Metabolism and Signaling: Role in Health and Diseases—2nd Edition)

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Open AccessReview

Genetic Variability in Child Growth Among South American Populations: A Perspective Integrating Population Genetics, Growth Standards, and Precision Growth Medicine

by Ana Karina Zambrano, Patricia Guevara-Ramírez, Santiago Cadena-Ullauri, Carmen Basantes, Susana Nicola, Susana Hidalgo and Maria L. Felix

Int. J. Mol. Sci. 2025, 26(19), 9300; https://doi.org/10.3390/ijms26199300 - 23 Sep 2025

Abstract

Child growth in South America results from a complex interplay of genetic, environmental, and socioeconomic factors. The region’s high ancestral diversity—stemming from Native American, European, and African admixture—shapes growth patterns in ways not fully captured by international standard curves such as World Health [...] Read more.

Child growth in South America results from a complex interplay of genetic, environmental, and socioeconomic factors. The region’s high ancestral diversity—stemming from Native American, European, and African admixture—shapes growth patterns in ways not fully captured by international standard curves such as World Health Organization (WHO) charts, which are primarily based on European population. This mismatch may cause misclassification, especially among Native American and other underrepresented groups, and reduce the effectiveness of interventions like growth hormone (GH) therapy. Evidence from national surveys, cohort studies, and genetic analyses reveals persistent ethnic and socioeconomic disparities, with Native American children showing higher stunting prevalence even after adjusting for wealth and residence. Differences between WHO and national growth curves further contribute to inconsistent prevalence estimates due to methodological and contextual variants. Regional genomic studies, although limited, have identified population-specific variants, such as FBN1 (E1297G) in Peru, and modulators of GH therapy response, including GHR exon 3 deletion, ACAN, and NPR2, highlighting the role of genetic background, treatment timing, and adherence in height outcomes. These findings underscore the need to move toward precision growth medicine, integrating anthropometry, genetic, environmental, and socioeconomic data to design population-specific growth references, optimize pharmacogenetic approaches, and reduce inequities in pediatric growth care. Full article

(This article belongs to the Special Issue Growth Hormone Deficiency: Molecular Pathologies and Therapeutic Strategies)

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Open AccessArticle

Evaluation of Inflammatory Markers in Perception Disorders in Major Psychiatric Pathology

by Laura-Maria Segarceanu, Andrei-Gabriel Zanfir, Dana Galieta Minca and Simona Trifu

Int. J. Mol. Sci. 2025, 26(19), 9299; https://doi.org/10.3390/ijms26199299 - 23 Sep 2025

Abstract

This study investigates the role of inflammatory markers in perception disorders associated with major psychiatric pathology, focusing on schizophrenia and acute psychotic disorder. Guided by the vulnerability–stress–inflammation model, this research explores how genetic predispositions, maternal immune activation, and chronic low-grade neuroinflammation contribute to [...] Read more.

This study investigates the role of inflammatory markers in perception disorders associated with major psychiatric pathology, focusing on schizophrenia and acute psychotic disorder. Guided by the vulnerability–stress–inflammation model, this research explores how genetic predispositions, maternal immune activation, and chronic low-grade neuroinflammation contribute to disease onset and progression. A sample of 135 patients (69 with schizophrenia and 66 with acute psychotic disorder) admitted to a psychiatric hospital between October 2024 and February 2025 was analyzed. Demographic and clinical data, along with biological markers—such as white blood cells, neutrophil-to-lymphocyte ratio (NLR), monocyte-to-lymphocyte ratio (MLR), platelet-to-lymphocyte ratio (PLR), systemic immune–inflammation index (SII), C-reactive protein (CRP), and erythrocyte sedimentation rate (ESR)—were assessed. Results indicated elevated median values for SII, CRP, and MLR, with statistically significant differences compared to normal reference ranges, suggesting persistent systemic inflammation in psychotic disorders. While acute psychotic disorders showed wider value ranges, schizophrenia patients demonstrated higher median levels, consistent with chronic inflammation. No significant differences were observed between the two groups after Bonferroni correction, though CRP values suggested a trend toward greater inflammation in schizophrenia. These findings reinforce the inflammatory hypothesis of psychosis and highlight the potential of biomarkers to refine diagnosis, guide treatment strategies, and support future research into immunomodulatory therapies. Full article

(This article belongs to the Section Molecular Neurobiology)

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Open AccessArticle

Study on the Molecular Mechanism of Arbuscular Mycorrhizal Symbiosis Regulating Polysaccharide Synthesis in Dendrobium officinale

by Jiadong Chen, Yiqun Zhang, Man Zhang, Ziyi Zhang, Yingying Liu, Xiaojing Duan, Zhengming Tao and Wu Jiang

Int. J. Mol. Sci. 2025, 26(19), 9298; https://doi.org/10.3390/ijms26199298 - 23 Sep 2025

Abstract

Mycorrhizal symbiosis represents a ubiquitous mutualistic relationship in nature, wherein mycorrhizal fungi enhance the host plant’s ability to absorb water and nutrients from the soil. In return, the host plant supplies the fungi with essential nutrients necessary for their metabolic activities. However, research [...] Read more.

Mycorrhizal symbiosis represents a ubiquitous mutualistic relationship in nature, wherein mycorrhizal fungi enhance the host plant’s ability to absorb water and nutrients from the soil. In return, the host plant supplies the fungi with essential nutrients necessary for their metabolic activities. However, research focusing on the regulatory mechanisms governing mycorrhizal symbiosis in Dendrobium officinale remains limited. This study systematically investigates the regulatory mechanisms of mycorrhizal symbiosis on transcriptional synthesis in D. officinale by establishing a mycorrhizal symbiotic system, complemented by phenotypic observation, physiological measurement, and transcriptome sequencing. The results indicate that mycorrhizal symbiosis promotes both growth and nutrient absorption in D. officinale, concurrently increasing polysaccharide content. Through transcriptome analysis, we identified 59 differentially expressed genes associated with polysaccharide metabolism, alongside key genes and transcription factors integral to the regulatory network. Notably, the glycosyltransferase gene DoUGT83A1 was found to negatively regulate the mycorrhizal symbiotic system when heterologously expressed in tomato. This study provides a fundamental theoretical basis for elucidating the molecular mechanisms underlying polysaccharide synthesis in D. officinale and offers new insights for optimizing cultivation practices to enhance medicinal quality. Full article

(This article belongs to the Section Molecular Plant Sciences)

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Open AccessArticle

Neuroprotective Effects of Vesatolimod in EAE: Modulating Immune Balance and Microglial Polarization

by Xueyu Chen, Jian Zhang and Shuhua Mu

Int. J. Mol. Sci. 2025, 26(19), 9297; https://doi.org/10.3390/ijms26199297 - 23 Sep 2025

Abstract

Multiple sclerosis (MS) is a chronic autoimmune disease characterized by sustained neuroinflammation and demyelination within the central nervous system (CNS). Vesatolimod (VES), a selective Toll-like receptor 7 (TLR7) agonist, has demonstrated both antiviral and immunomodulatory properties; however, its potential therapeutic value in neuroinflammatory [...] Read more.

Multiple sclerosis (MS) is a chronic autoimmune disease characterized by sustained neuroinflammation and demyelination within the central nervous system (CNS). Vesatolimod (VES), a selective Toll-like receptor 7 (TLR7) agonist, has demonstrated both antiviral and immunomodulatory properties; however, its potential therapeutic value in neuroinflammatory contexts remains poorly understood. In this study, we evaluated the efficacy of VES in the experimental autoimmune encephalomyelitis (EAE) model of MS and elucidated its mechanisms of action. EAE was induced in mice by immunization with myelin oligodendrocyte glycoprotein (MOG_35–55). The therapeutic effects of VES were assessed through clinical scoring, body weight monitoring, histopathology, flow cytometry, quantitative proteomics, and Western blot analysis. Additionally, an in vitro model of lipopolysaccharide (LPS)-induced microglial activation was employed to investigate cell-autonomous mechanisms. Results showed that VES administration significantly ameliorated disease severity, reduced weight loss, and enhanced neurological function in EAE mice. Treatment with VES inhibited the differentiation of pro-inflammatory Th1 and Th17 cells while expanding regulatory T cell (Treg) populations. It also preserved blood–brain barrier (BBB) integrity, attenuated demyelination, and modulated microglial activation phenotypes within the CNS. At the molecular level, VES activated the Nrf2/HO-1 antioxidant pathway, thereby enhancing the expression of cytoprotective proteins. Proteomic profiling further revealed the downregulation of inflammation-related proteins, specifically those associated with TNF, IL-17, and NOD-like receptor signaling pathways. Collectively, these findings demonstrate that VES alleviates neuroinflammation in EAE through multimodal mechanisms—including peripheral and central immune regulation, BBB protection, and activation of endogenous antioxidant defenses—supporting its further development as a promising therapeutic candidate for MS. Full article

(This article belongs to the Special Issue Molecular Advances and Perspectives in Multiple Sclerosis)

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Open AccessArticle

Hepatocyte Growth Factor-Mediated Chondrocyte Proliferation Induced by Adipose-Derived MSCs from Osteoarthritis Patients and Its Synergistic Enhancement by Hyaluronic Acid

by Samuel Jaeyoon Won, Hyun-Joo Lee, Dae-Yong Kim, Hyeonjeong Noh, Song yi Lee, Ji Ae Yoo, Yoon Sang Jeon, Heebeom Shin and Dong Jin Ryu

Int. J. Mol. Sci. 2025, 26(19), 9296; https://doi.org/10.3390/ijms26199296 - 23 Sep 2025

Abstract

Mesenchymal stem cells (MSCs) spontaneously assemble into three-dimensional (3D) spheroids under matrix-deficient conditions such as the synovial cavity, although their functional significance has yet to be fully elucidated. In this study, we used concave microwell cultures to promote the spontaneous aggregation of adipose-derived [...] Read more.

Mesenchymal stem cells (MSCs) spontaneously assemble into three-dimensional (3D) spheroids under matrix-deficient conditions such as the synovial cavity, although their functional significance has yet to be fully elucidated. In this study, we used concave microwell cultures to promote the spontaneous aggregation of adipose-derived MSCs (ASCs) from OA patients, thereby mimicking the intra-articular microenvironment. We analyzed the paracrine factors of ASC aggregates and compared it with that of conventional 2D monolayer cultures. Notably, 3D aggregation significantly increased the secretion of HGF and VEGF, whereas FGF2 levels remained relatively unchanged. These results indicate that the structural characteristics of ASC aggregates enhance the secretion of key paracrine factors involved in angiogenesis and tissue repair. To functionally evaluate the biological relevance of the secreted factors, conditioned media (CM) from ASC aggregates were applied to human articular chondrocytes. The CM significantly promoted chondrocyte proliferation, an effect that was abolished by the addition of HGF-neutralizing antibodies, thereby highlighting HGF as a central mediator of the regenerative response. Additionally, we further explored whether extracellular factors could modulate growth factor expression such as HGF. In this context, we investigated the impact of low-concentration hyaluronic acid (HA), a key synovial component widely used in OA treatment. Co-treatment with HA not only amplified the expression and secretion of HGF, VEGF, and FGF2, but also promoted ASC proliferation. ASCs forming functional aggregates may exert regenerative effects as active paracrine modulators, and the addition of low-dose hyaluronic acid is expected to further enhance this function, offering a promising strategy for MSC-based osteoarthritis therapy. Full article

(This article belongs to the Special Issue Stem Cells in Health and Disease: 3rd Edition)

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Open AccessArticle

A Maternal and Postnatal Ad Libitum Propionic Acid-Rich Diet in Mice Alters Intestinal Glia Proliferation and Inflammatory Response: Contrary to Effect in the Brain

by Piotr P. Lagod, Latifa S. Abdelli and Saleh A. Naser

Int. J. Mol. Sci. 2025, 26(19), 9295; https://doi.org/10.3390/ijms26199295 - 23 Sep 2025

Abstract

We previously demonstrated that propionic acid (PPA), a common food preservative and a metabolic byproduct of bacteria in dysbiosis (as seen in individuals affected with autism spectrum disorder, ASD), can lead to increased brain astrocyte proliferation and neuroinflammation in mice. We also showed [...] Read more.

We previously demonstrated that propionic acid (PPA), a common food preservative and a metabolic byproduct of bacteria in dysbiosis (as seen in individuals affected with autism spectrum disorder, ASD), can lead to increased brain astrocyte proliferation and neuroinflammation in mice. We also showed that in vitro treatment of human neural stem cells with PPA increased glial cell vs. neuron differentiation and yielded a marked increase in pro-inflammatory cytokines. In this study, a group of mice (FVB/N-Tg(GFAPGFP)14Mes/J) was exposed in utero through the maternal diet and postnatally ad libitum to a PPA-rich diet, while the control group was fed a normal diet. Intestinal tissue from offspring mice at 1 month (1 M) and 5 months (5 M) were then studied for neurodifferentiation and gastrointestinal (GI) inflammation. There was a significant increase in GFAP (Glial fibrillary acidic protein) expression (1.5427-fold and 1.6097-fold in 1 M and 5 M, respectively) and GFAP protein levels (1.5616-fold and 1.6701-fold in 1 M and 5 M, respectively) in the PPA group mice. It is worth mentioning that the expression level of intestinal astrocyte markers in the PPA group was significantly and multi-fold lower than that in the brain tissue. Contrary to data from brain tissue, the expression of pro-inflammatory cytokines in the PPA group decreased in intestinal tissue at 5 M (IL-6: 0.4403-fold; TNF-α: 0.4007-fold), while IL-10 expression and protein levels increased (1.9360-fold and 1.3428-fold, respectively). The data demonstrates that although there was a significant increase in GFAP in the intestine suggesting gliosis, there was an overall anti-inflammatory cytokine profile. The effect of PPA on intestinal cytokines is most likely in part due to the lower expression of GFAP in the enteric nervous system than the central nervous system (and the lower number of intestinal glia than astrocytes in the brain) and the dominance of intestinal macrophages and other immune cells compared to that in the brain. The overall finding strongly suggests that the PPA-rich diet affects the enteric glia state as shown by an increase in GFAP; however, it maintains the overall anti-inflammatory cytokine profile, possibly due to M2 macrophage polarization. Full article

(This article belongs to the Special Issue Interplay Between the Human Microbiome and Diseases)

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Open AccessReview

Genome Editing by Grafting

by Samuel Simoni, Marco Fambrini, Claudio Pugliesi and Ugo Rogo

Int. J. Mol. Sci. 2025, 26(19), 9294; https://doi.org/10.3390/ijms26199294 - 23 Sep 2025

Abstract

Grafting is the process of joining parts of two plants, allowing the exchange of molecules such as small RNAs (including microRNAs and small interfering RNAs), messenger RNAs, and proteins between the rootstock and the scion. Genome editing by grafting exploits RNAs, such as [...] Read more.

Grafting is the process of joining parts of two plants, allowing the exchange of molecules such as small RNAs (including microRNAs and small interfering RNAs), messenger RNAs, and proteins between the rootstock and the scion. Genome editing by grafting exploits RNAs, such as tRNA-like sequences (TLS motifs), to deliver the components (RNA) of the clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) system from transgenic rootstock to wild-type scion. The complex Cas9 protein and sgRNA-TLS produced in the scion perform the desired modification without the integration of foreign DNA in the plant genome, resulting in heritable transgene-free genome editing. In this review, we examine the current state of the art of this innovation and how it helps address regulatory problems, improves crop recovery and selection, exceeds the usage of viral vectors, and may reduce potential off-target effects. We also discuss the promise of genome editing by grafting for plants recalcitrant to in vitro culture and for agamic-propagated species that must maintain heterozygosity for plant productivity, fruit quality, and adaptation. Furthermore, we explore the limitations of this technique, including variable efficiency, graft incompatibility among genotypes, and challenges in large-scale application, while highlighting its considerable potential for further improvement and future broader applications for crop breeding. Full article

(This article belongs to the Section Molecular Genetics and Genomics)

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Open AccessReview

Nutritional Characteristics, Health-Related Properties, and Food Application of Teff (Eragrostis tef): An Overview

by Boyiza Samson Abebe, Iuliana Aprodu, Daniela Ionela Istrati and Camelia Vizireanu

Int. J. Mol. Sci. 2025, 26(19), 9293; https://doi.org/10.3390/ijms26199293 - 23 Sep 2025

Abstract

Teff [Eragrostis tef (Zucc.) Trotter] is a globally recognized ancient grain renowned for its attractive nutritional profile and diverse potential applications. Considering its physicochemical characteristics, nutritional value, and probable applications is essential for optimizing its benefits across various food industries. This review [...] Read more.

Teff [Eragrostis tef (Zucc.) Trotter] is a globally recognized ancient grain renowned for its attractive nutritional profile and diverse potential applications. Considering its physicochemical characteristics, nutritional value, and probable applications is essential for optimizing its benefits across various food industries. This review aims to comprehensively investigate teff, its physicochemical characteristics, diverse dietary applications, and health benefits. Teff is rich in macro- and micronutrients, making it an excellent addition to various food products. Bioactive compounds, such as flavonoids and phenolic acids, also enhance their functionality. Therefore, teff appears to be a whole grain with favorable technological characteristics and nutritional benefits for various food applications. Also, being gluten-free, teff is acceptable for individuals with celiac disease or gluten sensitivity. Also, it reduces cholesterol levels, supports heart health, stabilizes blood sugar levels, strengthens bone density and strength, and provides immune system support. In conclusion, teff shows excellent potential for developing innovative and nutritious solutions to meet the growing needs of consumers. Full article

(This article belongs to the Special Issue Role of Natural Compounds in Human Health and Disease)

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Open AccessArticle

Comprehensive Profiling of the miRNome and Degradome Reveals Regulatory Signatures of Seed Aging and Germination

by Marta Puchta-Jasińska, Paulina Bolc, Adrian Motor, Andreas Börner and Maja Boczkowska

Int. J. Mol. Sci. 2025, 26(19), 9292; https://doi.org/10.3390/ijms26199292 - 23 Sep 2025

Abstract

Small noncoding RNAs are recognized as crucial regulators of seed germination, but their role in seed aging remains unclear. To address this, we performed RNA sequencing (RNA-seq) on barley (Hordeum vulgare L.) seeds with varying viability levels after long-term storage in hermetically [...] Read more.

Small noncoding RNAs are recognized as crucial regulators of seed germination, but their role in seed aging remains unclear. To address this, we performed RNA sequencing (RNA-seq) on barley (Hordeum vulgare L.) seeds with varying viability levels after long-term storage in hermetically sealed containers since the 1972 harvest. This globally unique material, characterized by genetic homogeneity and contrasting germination capacities, enabled an in-depth analysis of microtranscriptomic changes during germination. We identified 62 known miRNAs from 11 families and 234 novel miRNAs, with miR159, miR168, and miR166 showing consistently high expression across all germination stages and viability groups. Differential expression analysis revealed 28 miRNAs whose abundance varied significantly with seed viability and germination phase. Functional predictions supported by quantitative reverse transcription PCR (qRT–PCR) and degradome-based target identification indicated that these miRNAs regulate key developmental and metabolic pathways. Several isomiRs exhibited sample-specific expression, suggesting the viability-dependent activation of distinct molecular mechanisms. Gene Ontology analysis highlighted processes related to nucleic acid binding, nuclear organization, and cytoplasmic metabolism as central during germination. We propose that miRNA profiles may reflect an “epigenetic inheritance”—a molecular memory of aging stored in seeds—rather than solely a response to current conditions. This concept may help explain aging-related phenotypes such as delayed germination and reduced vigor, warranting further investigation. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Genetics and Genomics in Poland: 3rd Edition)

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Open AccessArticle

Transcriptomic Analysis of TDP1-Knockout HEK293A Cells Treated with the TDP1 Inhibitor (Usnic Acid Derivative)

by Alexandra L. Zakharenko, Nadezhda S. Dyrkheeva, Andrey V. Markov, Maxim A. Kleshchev, Elena I. Ryabchikova, Anastasia A. Malakhova, Konstantin E. Orishchenko, Larisa S. Okorokova, Dmitriy N. Shtokalo, Sergey P. Medvedev, Suren M. Zakian, Alexey A. Tupikin, Marsel R. Kabilov, Olga A. Luzina, Sergey M. Deyev and Olga I. Lavrik

Int. J. Mol. Sci. 2025, 26(19), 9291; https://doi.org/10.3390/ijms26199291 - 23 Sep 2025

Abstract

Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a key enzyme for the repair of stalled topoisomerase 1 (TOP1)-DNA complexes. Previously, we obtained HEK293A cells with homozygous knockout of the TDP1 gene by the CRISPR/Cas9 method and used them as a cell model to study the [...] Read more.

Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a key enzyme for the repair of stalled topoisomerase 1 (TOP1)-DNA complexes. Previously, we obtained HEK293A cells with homozygous knockout of the TDP1 gene by the CRISPR/Cas9 method and used them as a cell model to study the mechanisms of anticancer therapy and to investigate the effect of TDP1 gene knockout on gene expression changes in the human HEK293A cell line by transcriptome analysis. In this study, we investigated the effect of a TDP1 inhibitor ((R,E)-2-acetyl-6-(2-(2-(4-bromobenzyliden) hydrazinyl) thiazol-4-yl)-3,7,9-trihydroxy-8,9b-dimethyldibenzo[b,d] furan-1(9bH)-one, OL9-119, an usnic acid derivative), capable of potentiating the antitumor effect of topotecan, as well as its combination with topotecan, on the transcriptome of wild-type and TDP1 knockout HEK293A cells. OL9-119 was found to be able to reduce cell motility by decreasing the expression of a number of genes, which may explain the antimetastatic effect of this compound. Differentially expressed genes (DEGs) related to electron transport, mitochondrial function, and protein folding were also identified under TDP1 inhibitor treatment. Full article

(This article belongs to the Special Issue New Agents and Novel Drugs Use for the Oncological Diseases Treatment)

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Open AccessReview

Gut Microbiome as a Source of Probiotic Drugs for Parkinson’s Disease

by Elena U Poluektova, Alla Stavrovskaya, Anastasia Pavlova, Roman Yunes, Maria Marsova, Tatiana Koshenko, Sergey Illarioshkin and Valery Danilenko

Int. J. Mol. Sci. 2025, 26(19), 9290; https://doi.org/10.3390/ijms26199290 - 23 Sep 2025

Abstract

Parkinson’s disease (PD) is a progressive, irreversible neurodegenerative disorder characterized by motor impairments and a wide spectrum of non-motor symptoms, including gastrointestinal dysfunction, sleep disturbances, depression, and cognitive decline. These manifestations arise from disturbances across multiple systems—gastrointestinal, neuroendocrine, immune, enteric, and central nervous [...] Read more.

Parkinson’s disease (PD) is a progressive, irreversible neurodegenerative disorder characterized by motor impairments and a wide spectrum of non-motor symptoms, including gastrointestinal dysfunction, sleep disturbances, depression, and cognitive decline. These manifestations arise from disturbances across multiple systems—gastrointestinal, neuroendocrine, immune, enteric, and central nervous systems. Alterations in the gut microbiota may play a causal role in PD onset and frequently accompany disease progression. The gut–brain axis, particularly the vagus nerve, is increasingly recognized as a key communication pathway whose dysregulation contributes to systemic dysfunction and the breakdown of homeostasis, ultimately driving PD pathology. Currently, there is no cure for PD, and existing treatments primarily target symptom relief. Effective management of PD requires a comprehensive approach that integrates multiple pharmacologically active agents aimed at restoring impaired organ functions and, when possible, neutralizing toxic factors that accelerate disease progression. One promising therapeutic avenue lies in functional gut bacteria, which form the basis for developing live biotherapeutic products, postbiotics, and bacterial vesicles. In this review, we summarize current data on the effects of probiotics in PD, drawing on both animal models and clinical studies. We highlight the role of probiotics in modulating PD pathophysiology and discuss their potential as adjunctive therapeutic agents. To provide a broader perspective, we also include sections describing the clinical manifestations of PD, gut microbiota alterations associated with the disease, and the role of artificial intelligence, particularly machine learning, in constructing functional models of PD. Full article

(This article belongs to the Section Molecular Microbiology)

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Open AccessArticle

Progressive Retinal Vascular and Neuronal Degeneration in BXD32 Mice: A Model for Age-Dependent Neurovascular Pathology

by Fan Xia, Shuizhen Shi, Seth E. Buscho, Erick Palacios, Melinda McCarty, Monia Nazemi, Lu Lu, Wenbo Zhang and Hua Liu

Int. J. Mol. Sci. 2025, 26(19), 9289; https://doi.org/10.3390/ijms26199289 - 23 Sep 2025

Abstract

Retinal vasculature is essential for maintaining visual function by supporting metabolically active neurons. However, the retina lacks redundant blood supply, rendering it highly susceptible to vascular dysfunction. Understanding mechanisms of retinal vascular abnormalities is critical for therapies that preserve vascular and neuronal integrity, [...] Read more.

Retinal vasculature is essential for maintaining visual function by supporting metabolically active neurons. However, the retina lacks redundant blood supply, rendering it highly susceptible to vascular dysfunction. Understanding mechanisms of retinal vascular abnormalities is critical for therapies that preserve vascular and neuronal integrity, yet progress has been hindered by limited models and genetic diversity. To address this gap, we examined the retinal vasculature in multiple aged strains from the BXD recombinant inbred mouse panel, a genetically diverse, tractable, and physiologically relevant platform for uncovering novel genetic drivers and disease mechanisms. We identified BXD32 as a striking outlier with dramatically reduced vessel density. Using optical coherence tomography, optical coherence tomography angiography, and histological analyses, we comprehensively characterized retinal vasculature and structural integrity of BXD32 mice during aging. We found progressive, age-dependent vascular dysfunction and degeneration, beginning in the deep capillary plexus and advancing to the intermediate and superficial layers. These changes were accompanied by neuronal degeneration, including photoreceptor loss and thinning of the ganglion cell complex. Our findings establish BXD32 as a spontaneous and genetically tractable model of inherited retinal neurovascular degeneration and provide a foundation for future studies to identify causative genetic loci and underlying molecular mechanisms. Full article

(This article belongs to the Special Issue Animal Research Model for Neurological Diseases, 2nd Edition)

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Open AccessArticle

HazChemNet: A Deep Learning Model for Hazardous Chemical Prediction

by Nan Zhang, Hexiang Qiu, Hongxia Cai, Zhiru Li, Yutong Li, Zinan Li, Lijuan Qi, Hongju Du, Yan Pan, Haiming Jing, Junyu Ning, Bo Xian and Shan Gao

Int. J. Mol. Sci. 2025, 26(19), 9288; https://doi.org/10.3390/ijms26199288 - 23 Sep 2025

Abstract

The identification of hazardous chemicals is critical for mitigating environmental and health risks, yet existing methods often lack efficiency and accuracy. This study presents HazChemNet, a deep learning model integrating attention-based autoencoders and mixture-of-experts architectures, designed to predict chemical hazardousness from molecular structures. [...] Read more.

The identification of hazardous chemicals is critical for mitigating environmental and health risks, yet existing methods often lack efficiency and accuracy. This study presents HazChemNet, a deep learning model integrating attention-based autoencoders and mixture-of-experts architectures, designed to predict chemical hazardousness from molecular structures. The study utilized a dataset of 2428 hazardous compounds from China’s 2015 hazardous chemical list. Features were derived from molecular fingerprints and physicochemical descriptors, with external validation on 52 unseen chemicals achieving 92.3% accuracy for hazardous and 84.6% for non-hazardous classifications. Experimental validation using C. elegans assays confirmed model predictions for critical compounds. Ablation studies confirmed hydrogen bonding features as pivotal predictors, alongside molecular fingerprints. This work bridges the gap between AI-driven innovation and chemical safety, offering a transformative tool for sustainable industrial practices and proactive risk management in a rapidly evolving global landscape. Full article

(This article belongs to the Special Issue Machine Learning and Bioinformatics in Human Health and Disease: 2nd Edition)

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