International Journal of Molecular Sciences

24 pages, 2286 KB

Open AccessArticle

APOE4 Alters Early Transcriptional Programs and Inflammatory Signaling in Human Induced Pluripotent Stem Cells

by Wiebke Schulten, Nele Johanne Czaniera, Mehran Fazel, Barbara Kaltschmidt and Christian Kaltschmidt

Int. J. Mol. Sci. 2026, 27(10), 4325; https://doi.org/10.3390/ijms27104325 (registering DOI) - 12 May 2026

Abstract

The APOE4 allele represents the strongest genetic risk factor for late-onset Alzheimer’s disease (AD), yet its influence on early cellular programs remains poorly understood. In this study, we investigated transcriptional differences between human induced pluripotent stem cells (iPSCs) carrying the APOE3 or APOE4 [...] Read more.

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

(This article belongs to the Special Issue Molecular Mechanisms and Signaling Pathways in Alzheimer’s Disease)

14 pages, 4189 KB

Open AccessArticle

A High-Molecular-Weight Fraction of Planarian Mucus Triggers UPR-Linked Cell Death Pathway in Human Bronchioalveolar Carcinoma Cell Line NCI-H358

by Gaetana Gambino, Gemma Marcelli, Paola Iacopetti, Laura Benvenuti, Chiara Bertini, Lucia Giambastiani, Luisa Pozzo, Alessandra Salvetti and Leonardo Rossi

Int. J. Mol. Sci. 2026, 27(10), 4324; https://doi.org/10.3390/ijms27104324 (registering DOI) - 12 May 2026

Abstract

Natural products remain a major source of anticancer agents, yet freshwater organisms are largely unexplored. Building on our previous evidence that planarian mucus exerts cytostatic and cytotoxic effects on cancer cells, we investigated the involvement of endoplasmic reticulum stress and unfolded protein response [...] Read more.

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

(This article belongs to the Special Issue Breakthroughs in Anti-Cancer Agents Discovery)

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64 pages, 4280 KB

Open AccessReview

The Mechanistic Review of the Molecular Interface of RNA-Loaded Extracellular Vesicles: Redefining Targeted Therapy for Autoimmune Disorders

by Aliya Orassay, Naizabek Yerzhigit, Anastassiya Ganina, Elmira Chuvakova, Oleg Lookin and Abay Baigenzhin

Int. J. Mol. Sci. 2026, 27(10), 4323; https://doi.org/10.3390/ijms27104323 - 12 May 2026

Abstract

Traditional treatments of autoimmune diseases relying on systemic immunosuppression often lack curative potential and have severe side effects. Mesenchymal stem cells (MSCs) are a promising alternative due to their immunomodulatory properties; however, whole-cell therapies have certain limitations. MSC-derived extracellular vesicles (EVs), including small [...] Read more.

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

(This article belongs to the Section Molecular Immunology)

29 pages, 2218 KB

Open AccessReview

Immunosenescence and Bone Homeostasis: From Mechanisms of Homeostasis Disruption to Therapeutic Opportunities in Age-Related Skeletal Disorders

by Fuhan Jiang, Bowen Dong, Yijue Wang and Yi Xiong

Int. J. Mol. Sci. 2026, 27(10), 4322; https://doi.org/10.3390/ijms27104322 - 12 May 2026

Abstract

The progressive decline in immune function during aging, termed immunosenescence, is increasingly recognized as a critical driver of skeletal fragility and impaired bone regeneration. This age-associated phenomenon—driven by thymic involution, inflammaging, and the accumulation of senescent immune cells—disrupts bone homeostasis primarily through the [...] Read more.

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

(This article belongs to the Section Molecular Immunology)

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19 pages, 3417 KB

Open AccessArticle

SKNY-1, a THCV Analog, Produces Weight Loss, Lipid Normalization and Attenuation of Reward-Associated Behaviors in an mc4r(G894C) Zebrafish Model of Obesity

by Itzchak Angel, Kalaichitra Periyasamy, Benin Joseph and Erez Aminov

Int. J. Mol. Sci. 2026, 27(10), 4321; https://doi.org/10.3390/ijms27104321 - 12 May 2026

Abstract

Obesity resulting from melanocortin-4 receptor (MC4R) dysfunction is characterized by combined metabolic dysregulation and maladaptive reward-related behaviors that limit the durability of existing therapies. The endocannabinoid system is a central regulator of appetite, lipid metabolism, and reward processing; however, first-generation cannabinoid receptor 1 [...] Read more.

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

(This article belongs to the Section Molecular Endocrinology and Metabolism)

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32 pages, 2380 KB

Open AccessArticle

Small Extracellular Vesicle Release Following Electrical Pulse Stimulation of C2C12 Myotubes: Effects on microRNA Cargo and Myoblast Migration and Differentiation

by John S. Hingle, Rhys S. McColl, Ivan J. Vechetti and Kathryn H. Myburgh

Int. J. Mol. Sci. 2026, 27(10), 4320; https://doi.org/10.3390/ijms27104320 - 12 May 2026

Abstract

The skeletal muscle (SkM) secretome has been widely studied since the establishment of its endocrine function. Extracellular vesicles (EVs) are the most recently identified elements of the SkM secretome. These nano-sized lipid-bound vesicles carry molecular cargo and function as a means of intercellular [...] Read more.

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

(This article belongs to the Special Issue Current Insights into the Role of Exosomes in Intercellular Communication, 2nd Edition)

13 pages, 659 KB

Open AccessArticle

Host Immune Responses to SARS-CoV-2 Vaccination in Northern Mexico: Structural Biology Insights and the Impact of Obesity

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

Int. J. Mol. Sci. 2026, 27(10), 4319; https://doi.org/10.3390/ijms27104319 - 12 May 2026

Abstract

Understanding the molecular mechanisms underlying host immune responses to SARS-CoV-2 vaccination remains essential, particularly in populations with a high prevalence of obesity. In this cross-sectional study, we evaluated whether body mass index (BMI) is associated with vaccine-induced humoral immunity in a cohort from [...] Read more.

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

(This article belongs to the Section Molecular Immunology)

21 pages, 2962 KB

Open AccessArticle

Phylogeography and Population Structure of the Invasive Land Snail Monacha cartusiana

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

Int. J. Mol. Sci. 2026, 27(10), 4318; https://doi.org/10.3390/ijms27104318 - 12 May 2026

Abstract

Monacha cartusiana (O. F. Müller, 1774), native to the Mediterranean region and Europe, is a terrestrial gastropod recognized as a highly destructive agricultural pest that causes significant damage to crop plants, fruit trees, vegetables, ornamentals, and natural ecosystems. Despite its broad geographic distribution, [...] Read more.

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

(This article belongs to the Section Molecular Informatics)

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15 pages, 669 KB

Open AccessArticle

Mitochondrial Calcium Overload Drives mtDNA-cGAS-STING Activation via VDAC1 and MCU Upregulation in Periodontitis

by Xinyi Cheng, Yu Cai, Yiran Geng, Xiaoying Zang, Jia Liu and Qingxian Luan

Int. J. Mol. Sci. 2026, 27(10), 4317; https://doi.org/10.3390/ijms27104317 - 12 May 2026

Abstract

Periodontitis is a chronic inflammatory disease remaining elusive with its pathogenesis. Mitochondrial dysfunction and aberrant immune activation are implicated, but the underlying mechanisms remain incompletely understood. Given the essential role of Ca²⁺ homeostasis in maintaining normal mitochondrial function, we investigated the role [...] Read more.

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

(This article belongs to the Section Molecular Immunology)

27 pages, 1123 KB

Open AccessReview

Cellular Products with Anti-Inflammatory Properties for the Treatment of Cartilage Lesions

by Polina A. Golubinskaya, Evgenii S. Ruchko, Alexandra N. Bogomazova and Artem V. Eremeev

Int. J. Mol. Sci. 2026, 27(10), 4316; https://doi.org/10.3390/ijms27104316 - 12 May 2026

Abstract

Most high-tech drugs and tissue engineering products based on human chondrocytes currently available on the market are aimed at restoring traumatic damage to cartilage tissue. However, in the presence of inflammation, their regenerative potential is significantly reduced, which limits their use in patients [...] Read more.

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

(This article belongs to the Special Issue Modern Approaches in Regenerative Therapy)

22 pages, 1774 KB

Open AccessArticle

DDIT3 Promotes Starvation-Induced Autophagy via ER Stress in Vero Cells

by Muzi Li, Renhou Jia, Rong Huang, Jiamin Wang, Zilin Qiao and Na Sun

Int. J. Mol. Sci. 2026, 27(10), 4315; https://doi.org/10.3390/ijms27104315 - 12 May 2026

Abstract

Vero cells in high-density vaccine cultures often face nutrient starvation, especially in suspension-adapted Vero cells. Previous studies showed that serum starvation dramatically enhances autophagy and mitophagy in suspension-adapted Vero cells. Transcriptomic profiling also revealed significant upregulation of DDIT3, a marker of endoplasmic [...] Read more.

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

(This article belongs to the Section Molecular Biology)

16 pages, 3182 KB

Open AccessReview

Cylindrical Crystallization of Ca²⁺-ATPase and Its Potential Role in Sarcoplasmic Reticulum Dynamics

by Jun Nakamura, Genichi Tajima, Makiko Suwa and Chikara Sato

Int. J. Mol. Sci. 2026, 27(10), 4314; https://doi.org/10.3390/ijms27104314 - 12 May 2026

Abstract

How do ryanodine receptors (RyRs) open simultaneously to trigger the contraction of whole myofibrils within a large skeletal muscle cell? One possible answer is the uniformity of mechanosensitive RyRs, which is mechanically forced by the neighboring environment, including proteins. Here, we review papers [...] Read more.

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

(This article belongs to the Special Issue Structure and Function of Subcellular Organelle and Protein-Membrane Systems)

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37 pages, 841 KB

Open AccessReview

Recent Progress in Mechanism-Based Therapies for GJB2-Related Hearing Loss

by Chengzhi Liu, Xiaohui Wang and Yu Sun

Int. J. Mol. Sci. 2026, 27(10), 4313; https://doi.org/10.3390/ijms27104313 - 12 May 2026

Abstract

GJB2-associated hearing loss is the most common form of non-syndromic hereditary deafness worldwide. However, it exhibits significant heterogeneity in terms of both clinical presentation and biological basis. This review focuses on mechanism-oriented therapeutic strategies for GJB2-associated hearing loss, investigating how different [...] Read more.

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

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

7 pages, 548 KB

Open AccessCase Report

Myxoid Lipoblastoma with New Fusion Transcript CHCHD7::PLAG1 in an 18-Month-Old Girl Diagnosed by Target RNA Sequencing: A Case Report

by Danijela Cvetković, Marina Gazdić Janković, Marina Miletić Kovačević, Amra Ramović Hamzagić, Irena Urošević, Vesna Rosić and Biljana Ljujić

Int. J. Mol. Sci. 2026, 27(10), 4312; https://doi.org/10.3390/ijms27104312 - 12 May 2026

Abstract

Lipoblastomas are rare, benign tumors arising from embryonic white fatty precursor cells that continue to proliferate in the postnatal period. We present a case of a minimally differentiated lipoblastoma with myxoid features. Our patient was an 18-month-old female with a painless solid tumefaction [...] Read more.

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

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

19 pages, 310 KB

Open AccessReview

The Metabolic Architecture of Glaucoma: A Unified Framework of Cofactor Failure and Kynurenine Dysregulation

by Liva Caikovska, Alberts Veitners, Diana Lavrinovica, Juris Vanags, Kristaps Klavins, Guna Laganovska and Arturs Zemitis

Int. J. Mol. Sci. 2026, 27(10), 4311; https://doi.org/10.3390/ijms27104311 - 12 May 2026

Abstract

Glaucoma remains a primary cause of blindness, yet its pathogenesis often extends beyond intraocular pressure (IOP). This review integrates four converging lines of metabolic evidence—aqueous humor (AH) metabolomics, kynurenine pathway (KP) activity, tetrahydrobiopterin (H4BIP) biology, and NAD/one-carbon dysfunction—into a testable framework for retinal [...] Read more.

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

(This article belongs to the Special Issue Metabolomics as a Window into Human Disease Mechanisms)

22 pages, 14523 KB

Open AccessArticle

The Role and Mechanism of Nrf2 in Ameliorating Oxidative Stress and Inflammation in IR Mice by Aerobic Exercise

by Xuan Liu, Yuqing Ding, Tao Chen, Zhengkang Wu, Shujuan Hu and Xianwang Wang

Int. J. Mol. Sci. 2026, 27(10), 4310; https://doi.org/10.3390/ijms27104310 - 12 May 2026

Abstract

This study explored the regulatory role of nuclear factor E2-related factor 2 (Nrf2) in aerobic exercise improving oxidative stress and inflammatory responses in mice with insulin resistance (IR) induced by a high-fat diet. We established an IR mouse model through a high-fat diet, [...] Read more.

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

(This article belongs to the Section Molecular Immunology)

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31 pages, 9610 KB

Open AccessReview

Human Endogenous Retroviruses in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: Emerging Roles in Pathogenesis, Immunity, Biomarkers and Therapeutics

by Krishani Dinali Perera, Elisa Oltra Garcia and Simon R. Carding

Int. J. Mol. Sci. 2026, 27(10), 4309; https://doi.org/10.3390/ijms27104309 - 12 May 2026

Abstract

Human endogenous retroviruses (HERVs) are potential driving forces of the pathophysiology of Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), linking post-infectious immune dysfunction to chronic inflammation and immune and neurocognitive dysfunction that are hallmark features of ME/CFS. Accumulating evidence from related autoimmune diseases and cancers [...] Read more.

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

(This article belongs to the Special Issue Molecular Pathologies and Treatment for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome—2nd Edition)

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18 pages, 922 KB

Open AccessArticle

Exosomal lncRNAs HOTAIR, HULC, and ANRIL: Decoding the Biomarker Landscape of Sporadic Triple-Negative Breast Cancer

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

Int. J. Mol. Sci. 2026, 27(10), 4308; https://doi.org/10.3390/ijms27104308 - 12 May 2026

Abstract

Triple-negative breast cancer (TNBC/18–21%) lacks targeted treatment options due to the lack of ER/PR and HER2 expression. The transport of lncRNAs via exosomes plays a role in tumor progression and metastasis and reshapes tumor-associated signaling pathways. This study aimed to compare the expression [...] Read more.

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

(This article belongs to the Special Issue Recent Advances in Non-Coding RNAs in Human Research)

15 pages, 2380 KB

Open AccessReview

Therapeutic Innovations for Monkeypox Inhibition

by Nayan De, Jhuma Bhadra, Md Sorique Aziz Momin, Kamala Mitra, Debmalya Bhunia and Achinta Sannigrahi

Int. J. Mol. Sci. 2026, 27(10), 4307; https://doi.org/10.3390/ijms27104307 - 12 May 2026

Abstract

This review investigates biomaterial-based strategies for improved treatment of MPXV. We focus on emerging synthetic biomedical approaches to combating the virus. These include peptide nucleic acids, CRISPR-based systems, and small-molecule therapeutics. These methods work by targeting and blocking viral proteins and enzymes. Such [...] Read more.

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

(This article belongs to the Special Issue Molecular Advances in Zoonoses and Vector-Borne Diseases)

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