International Journal of Molecular Sciences

13 pages, 7067 KiB

Open AccessArticle

The Effect of Rosavin, a Characteristic Compound of Rhodiola rosea, on BMP-2 Induction and Osteoblast Proliferation In Vitro

by Piotr Wojdasiewicz, Edyta Wróbel, Krzysztof Stolarczyk, Elżbieta U. Stolarczyk, Agnieszka Mikulska and Dariusz Szukiewicz

Int. J. Mol. Sci. 2025, 26(13), 6075; https://doi.org/10.3390/ijms26136075 - 24 Jun 2025

Abstract

Rosavin, a glycoside isolated from Rhodiola rosea, exhibits various biological activities, including potential modulation of metabolic pathways. Despite promising findings in animal models, its effects on many human bone cells remain unexplored. This study aimed to investigate, for the first time, the [...] Read more.

Rosavin, a glycoside isolated from Rhodiola rosea, exhibits various biological activities, including potential modulation of metabolic pathways. Despite promising findings in animal models, its effects on many human bone cells remain unexplored. This study aimed to investigate, for the first time, the in vitro effects of rosavin on human osteoblasts (HOBs), focusing on BMP-2 expression, cell morphology, and culture confluence as indicators of osteogenic activity. HOB cultures were treated with 50 µM or 100 µM rosavin for 21 days. BMP-2 expression was measured by ELISA, collagen production was assessed via Sirius Red staining, and cell morphology and confluence were evaluated using phase-contrast microscopy. A significant increase in BMP-2 expression was observed in the 100 µM rosavin group compared to the mineralization control (p < 0.05), particularly on days 14 and 21. Both rosavin-treated groups exhibited higher confluence than controls, with the 50 µM group showing unexpectedly greater confluence than the 100 µM group. Rosavin at 50 µM also promoted a cuboidal morphology characteristic of active HOBs. The presence of collagen validated both the successful progression of the mineralization process and the correct implementation of the experimental protocol. Rosavin enhances BMP-2 expression and supports HOB proliferation and morphological maturation in vitro. These findings suggest its potential as a supportive agent in the prevention or treatment of metabolic bone diseases. Further research is necessary to determine its bioavailability, safety profile, and therapeutic relevance in clinical settings. Full article

(This article belongs to the Special Issue Medicinal Plants and Bioactive Compounds in Health and Disease)

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11 pages, 5852 KiB

Open AccessArticle

Structural Insights into the Regulatory Mechanisms of the Toxic Activity of Sofic in Anti-Phage Defense Systems

by Zhuoxi Wu, Guodong Chen, Libang He, Hao Guo, Ruifang Yuan, Huiling Su, Zhenyang Xie and Faxiang Li

Int. J. Mol. Sci. 2025, 26(13), 6074; https://doi.org/10.3390/ijms26136074 - 24 Jun 2025

Abstract

The FIC domain-containing protein Sofic has recently been shown to provide robust protection to bacteria against phage infection. Sofic acts as a toxic protein, inducing abortive infection through the AMPylation of target proteins during phage invasion. However, the molecular mechanisms regulating Sofic’s toxic [...] Read more.

The FIC domain-containing protein Sofic has recently been shown to provide robust protection to bacteria against phage infection. Sofic acts as a toxic protein, inducing abortive infection through the AMPylation of target proteins during phage invasion. However, the molecular mechanisms regulating Sofic’s toxic activity remain elusive. In this study, we identified a small gene encoding a short protein located downstream of Sofic in the genome, named AS1 (anti-Sofic1), which functions as an antitoxic protein to counteract Sofic’s toxicity. The crystal structure of Sofic revealed that the protein functions as a dimer in solution, with dimerization being indispensable for its toxic activity. Importantly, structural analysis indicated that ATP binding induces a conformational change in the C-terminal domain (CTD) of Sofic, underscoring the critical role of the CTD in mediating its toxic effects. In vitro colony-forming assays confirmed that the interaction between the CTD and the Amylase domain is crucial for Sofic’s toxic activity. Overall, our results provide molecular insights into the regulatory mechanisms of Sofic in antiviral immunity. Full article

(This article belongs to the Section Molecular Microbiology)

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17 pages, 824 KiB

Open AccessArticle

Preclinical Evaluation of the Systemic Safety, Efficacy, and Biodistribution of a Recombinant AAV8 Vector Expressing FIX-TripleL in Hemophilia B Mice: Implications for Human Gene Therapy

by Sheng-Chieh Chou, Cheng-Po Huang, Ying-Hui Su, Chih-Hsiang Yu, Yung-Li Yang, Ssu-Chia Wang, Yi-Hsiu Lin, Yen-Ting Chen, Jia-Yi Li, Yen-Ting Chang, Su-Yu Chen and Shu-Wha Lin

Int. J. Mol. Sci. 2025, 26(13), 6073; https://doi.org/10.3390/ijms26136073 - 24 Jun 2025

Abstract

Gene therapy for hemophilia B offers the advantage of a single administration with sustained therapeutic effects. This study evaluated the systemic safety, efficacy, biodistribution, and immunogenicity of AAV8-FIX-TripleL, a recombinant adeno-associated virus type 8 (AAV8) vector encoding a modified factor IX (FIX) variant [...] Read more.

Gene therapy for hemophilia B offers the advantage of a single administration with sustained therapeutic effects. This study evaluated the systemic safety, efficacy, biodistribution, and immunogenicity of AAV8-FIX-TripleL, a recombinant adeno-associated virus type 8 (AAV8) vector encoding a modified factor IX (FIX) variant with increased activity. In this good laboratory practice (GLP)-compliant study, 180 male FIX-knockout hemophilia B mice were randomized into 12 groups (n = 15) and received intravenous AAV8-FIX-TripleL at therapeutic (5 × 10¹¹ VG/kg) or supraphysiological (5 × 10¹² VG/kg) doses on Day 1. The mice were sacrificed on Days 2, 15, 28, and 91 for comprehensive evaluations, including hematological and biochemical assessments, histopathological examination, FIX protein/activity analysis, immunogenicity assessment, and vector biodistribution via quantitative polymerase chain reaction (qPCR) in major organs. AAV8-FIX-TripleL demonstrated dose-dependent increases in FIX activity and protein levels, with FIX activity exceeding physiological levels and the maintenance of a favorable safety profile. Biodistribution analysis confirmed predominant hepatic accumulation and vector persistence up to 91 days post-injection, with minimal off-target distribution. These findings indicate that AAV8-FIX-TripleL is a promising gene therapy candidate for hemophilia B, as it has robust expression, sustained efficacy, and a favorable safety profile, and that further translational studies are warranted. Full article

(This article belongs to the Special Issue Hemophilia: From Pathophysiology to Novel Therapies)

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22 pages, 1664 KiB

Open AccessArticle

Epigenetic Remodeling of Regulatory Regions by Indicaxanthin Suggests a Shift in Cell Identity Programs in Colorectal Cancer Cells

by Maria Antonietta Ragusa, Carla Gentile, Aldo Nicosia, Salvatore Costa, Sara Volpes, Laura Greco, Flores Naselli and Fabio Caradonna

Int. J. Mol. Sci. 2025, 26(13), 6072; https://doi.org/10.3390/ijms26136072 - 24 Jun 2025

Abstract

Aberrant DNA methylation is a hallmark of colorectal cancer (CRC), contributing to tumor progression through the silencing of tumor suppressor genes and activation of oncogenes. Indicaxanthin (IND), a dietary betalain pigment from Opuntia ficus indica, has shown antiproliferative effects in CRC models, [...] Read more.

Aberrant DNA methylation is a hallmark of colorectal cancer (CRC), contributing to tumor progression through the silencing of tumor suppressor genes and activation of oncogenes. Indicaxanthin (IND), a dietary betalain pigment from Opuntia ficus indica, has shown antiproliferative effects in CRC models, yet its epigenetic impact remains unexplored. In this study, we investigated the effects of IND on the methylome of Caco-2 cells using Reduced Representation Bisulfite Sequencing (RRBS). IND induced a global hypermethylation profile, particularly at gene promoters and CpG islands. Among the differentially methylated genes, 60% were protein-coding, and 10% encoded transcription factors, including PAX5 and TFAP4, both hypermethylated at active enhancers. Functional enrichment analysis revealed pathways beyond canonical intestinal functions, suggesting altered cell identity and plasticity. Transcription factor targets (SOX10, NFKB1, AHR, ARNT) were significantly enriched among the affected genes, several of which are involved in transdifferentiation processes. Methylation changes also indicated potential reprogramming toward epithelial cell types from pulmonary or neuroectodermal origin. Moreover, IND induced selective hypomethylation of Alu elements on chromosome 21 and hypermethylation of rDNA loci, hinting at suppressed ribosomal biogenesis. Overall, these findings highlight the epigenetic remodeling potential of IND and its possible role in modulating cell fate and metabolism in CRC cells. Full article

(This article belongs to the Special Issue Fundamental and Translational Insights into Colorectal Cancer)

12 pages, 2016 KiB

Open AccessArticle

Molecular Signatures of Dendritic Cell Activation upon TNF Stimulation: A Multi-Omics Study in Rheumatoid Arthritis

by Alina Alshevskaya, Shakir Suleimanov, Elizaveta Sheveleva, Roman Perik-Zavodskii, Olga Perik-Zavodskaia, Saleh Alrhmoun, Julia Lopatnikova, Julia Zhukova, Nadezhda Shkaruba, Natalia Sivitskaya, Alexey Sizikov, Elena Golikova and Sergey Sennikov

Int. J. Mol. Sci. 2025, 26(13), 6071; https://doi.org/10.3390/ijms26136071 - 24 Jun 2025

Abstract

Dendritic cells (DCs) play a central role in the immunopathogenesis of rheumatoid arthritis (RA), yet their regulation by tumor necrosis factor alpha (TNF) and associated receptors remains poorly characterized. We applied a single-cell multi-omics approach (CITE-seq) to profile peripheral blood mononuclear cells (PBMCs) [...] Read more.

Dendritic cells (DCs) play a central role in the immunopathogenesis of rheumatoid arthritis (RA), yet their regulation by tumor necrosis factor alpha (TNF) and associated receptors remains poorly characterized. We applied a single-cell multi-omics approach (CITE-seq) to profile peripheral blood mononuclear cells (PBMCs) from RA patients and healthy donors, before and after in vitro TNF stimulation. Using integrated analysis of surface protein expression and transcriptomic data, we focused on phenotypic and transcriptional changes in dendritic cell populations. DCs from RA patients exhibited elevated surface expression of CD14 and CD16, indicative of an inflammatory phenotype, and showed marked responsiveness to TNF. Upon stimulation, RA-derived DCs upregulated genes involved in antigen presentation (CD83, LAMP3), lymph node migration (CCR7, ADAM19), and inflammation (TRAF1, IL24) whereas such activation was absent in healthy controls. Our data reveal a TNF-responsive, pro-inflammatory transcriptional program in dendritic cells from RA patients and underscore the relevance of the TNF receptor profile in shaping DC function. These findings provide new insights into the immunobiology of RA and identify dendritic cells as potential targets for personalized immunomodulatory therapy. Full article

(This article belongs to the Special Issue Editorial Board Member's Collection Series: The Memory of the Immune Cells)

35 pages, 3359 KiB

Open AccessArticle

GSH/pH-Responsive Chitosan–PLA Hybrid Nanosystems for Targeted Ledipasvir Delivery to HepG2 Cells: Controlled Release, Improved Selectivity, DNA Interaction, Electrochemical and Stopped-Flow Kinetics Analyses

by Ahmed M. Albasiony, Amr M. Beltagi, Mohamed M. Ibrahim, Shaban Y. Shaban and Rudi van Eldik

Int. J. Mol. Sci. 2025, 26(13), 6070; https://doi.org/10.3390/ijms26136070 - 24 Jun 2025

Abstract

This study aimed to design dual-responsive chitosan–polylactic acid nanosystems (PLA@CS NPs) for controlled and targeted ledipasvir (LED) delivery to HepG2 liver cancer cells, thereby reducing the systemic toxicity and improving the therapeutic selectivity. Two formulations were developed utilizing ionotropic gelation and w/ [...] Read more.

This study aimed to design dual-responsive chitosan–polylactic acid nanosystems (PLA@CS NPs) for controlled and targeted ledipasvir (LED) delivery to HepG2 liver cancer cells, thereby reducing the systemic toxicity and improving the therapeutic selectivity. Two formulations were developed utilizing ionotropic gelation and w/o/w emulsion techniques: LED@CS NPs with a size of 143 nm, a zeta potential of +43.5 mV, and a loading capacity of 44.1%, and LED-PLA@CS NPs measuring 394 nm, with a zeta potential of +33.3 mV and a loading capacity of 89.3%, with the latter demonstrating significant drug payload capacity. Since most drugs work through interaction with DNA, the in vitro affinity of DNA to LED and its encapsulated forms was assessed using stopped-flow and other approaches. They bind through multi-modal electrostatic and intercalative modes via two reversible processes: a fast complexation followed by a slow isomerization. The overall binding activation parameters for LED (cordination affinity, K_a = 128.4 M⁻¹, K_d = 7.8 × 10⁻³ M, ΔG = −12.02 kJ mol⁻¹), LED@CS NPs (K_a = 2131 M⁻¹, K_d = 0.47 × 10⁻³ M, ΔG = −18.98 kJ mol⁻¹) and LED-PLA@CS NPs (K_a = 22026 M⁻¹, K_d = 0.045 × 10⁻³ M, ΔG = −24.79 kJ mol⁻¹) were obtained with a reactivity ratio of 1/16/170 (LED/LED@CS NPs/LED-PLA@CS NPs). This indicates that encapsulation enhanced the interaction between the DNA and the LED-loaded nanoparticle systems, without changing the mechanism, and formed thermodynamically stable complexes. The drug release kinetics were assessed under tumor-mimetic conditions (pH 5.5, 10 mM GSH) and physiological settings (pH 7.4, 2 μM GSH). The LED@CS NPs and LED-PLA@CS NPs exhibited drug release rates of 88.0% and 73%, respectively, under dual stimuli over 50 h, exceeding the release rates observed under physiological conditions, which were 58% and 54%, thereby indicating that the LED@CS NPs and LED-PLA@CS NPs systems specifically target malignant tissue. Release regulated by Fickian diffusion facilitates tumor-specific payload delivery. Although encapsulation did not enhance the immediate cytotoxicity compared to free LED, as demonstrated by an in vitro cytotoxicity in HepG2 cancer cell lines, it significantly enhanced the therapeutic index (2.1-fold for LED-PLA@CS NPs) by protecting non-cancerous cells. Additionally, the nanoparticles demonstrated broad-spectrum antibacterial effects, suggesting efficacy in the prevention of chemotherapy-related infections. The dual-responsive LED-PLA@CS NPs allowed controlled tumor-targeted LED delivery with better selectivity and lower off-target toxicity, making LED-PLA@CS NPs interesting candidates for repurposing HCV treatments into safer cancer nanomedicines. Furthermore, this thorough analysis offers useful reference information for comprehending the interaction between drugs and DNA. Full article

(This article belongs to the Section Molecular Nanoscience)

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Graphical abstract

33 pages, 3479 KiB

Open AccessArticle

Transcriptomic Profiling of Zebrafish Mutant for cdkl5 Reveals Dysregulated Gene Expression Associated with Neuronal, Muscle, Visual and Skeletal Development

by Tatiana Varela, Débora Varela, Natércia Conceição and M. Leonor Cancela

Int. J. Mol. Sci. 2025, 26(13), 6069; https://doi.org/10.3390/ijms26136069 - 24 Jun 2025

Abstract

Zebrafish is a well-recognized model for studying human genetic disorders. Recently, we proposed the homozygous cdkl5^sa21938 mutant zebrafish as a model of CDKL5 deficiency disorder (CDD), a developmental epileptic encephalopathy with diverse symptoms. This study aimed to explore Cdkl5-associated molecular mechanisms in [...] Read more.

Zebrafish is a well-recognized model for studying human genetic disorders. Recently, we proposed the homozygous cdkl5^sa21938 mutant zebrafish as a model of CDKL5 deficiency disorder (CDD), a developmental epileptic encephalopathy with diverse symptoms. This study aimed to explore Cdkl5-associated molecular mechanisms in zebrafish and assess their similarity to those in mammals. We conducted RNA sequencing on whole cdkl5^−/− zebrafish and wild-type siblings at 5 and 35 days post-fertilization (dpf) to compare their gene expression profiles. Most significant differentially expressed genes (DEGs) were related to muscle, neuronal, and visual systems which are affected in CDD. Gene Ontology analysis revealed downregulated DEGs enriched in muscle development, extracellular matrix, and actin cytoskeleton functions at both stages, while upregulated DEGs were enriched in eye development functions at 35 dpf. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed enrichment of downregulated DEGs in focal adhesion and extracellular matrix (ECM)-receptor interaction pathways at both stages. Neuronal development DEGs were mainly downregulated at both stages, while synaptic signaling DEGs were upregulated at 35 dpf. Crossing cdkl5^−/− mutants with the Hb9:GFP transgenic line showed fewer motor neuron cells with shorter axons compared to the wild type, which may explain the impaired motor phenotype observed in zebrafish and CDD patients. Moreover, we identified key downregulated DEGs related to cartilage development at both stages and bone development at 35 dpf, potentially explaining the skeletal defects seen in zebrafish and CDD individuals. In conclusion, Cdkl5 loss in zebrafish leads to dysregulation of genes involved in CDKL5-associated functions in mammals, providing new insights into its less studied functions and phenotypes. Full article

(This article belongs to the Section Molecular Biology)

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20 pages, 2276 KiB

Open AccessArticle

Post-Transcriptional Regulation of the MiaA Prenyl Transferase by CsrA and the Small RNA CsrB in Escherichia coli

by Joseph I. Aubee, Kinlyn Williams, Alexandria Adigun, Olufolakemi Olusanya, Jalisa Nurse and Karl M. Thompson

Int. J. Mol. Sci. 2025, 26(13), 6068; https://doi.org/10.3390/ijms26136068 - 24 Jun 2025

Abstract

MiaA is responsible for the addition of the isopentyl modification to adenine 37 in the anticodon stem loop of specific tRNAs in Escherichia coli. Mutants in miaA have pleotropic effects on the cell in E. coli and play a role in virulence [...] Read more.

MiaA is responsible for the addition of the isopentyl modification to adenine 37 in the anticodon stem loop of specific tRNAs in Escherichia coli. Mutants in miaA have pleotropic effects on the cell in E. coli and play a role in virulence gene regulation. In addition, MiaA is necessary for stress response gene expression by promoting efficient decoding of UUX-leucine codons, and genes with elevated UUX-leucine codons may be a regulatory target for i⁶A-modified tRNAs. Understanding the temporal nature of the i⁶A modification status of tRNAs would help us determine the regulatory potential of MiaA and its potential interplay with leucine codon frequency. In this work, we set out to uncover additional information about the synthesis of the MiaA. MiaA synthesis is primarily driven at the transcriptional level from multiple promoters in a complex operon. However, very little is known about the post-transcriptional regulation of MiaA, including the role of sRNAs in its synthesis. To determine the role of small RNAs (sRNAs) in the regulation of miaA, we constructed a chromosomal miaA-lacZ translational fusion driven by the arabinose-responsive P_BAD promoter and used it to screen against an Escherichia coli sRNA library (containing sRNAs driven by the IPTG-inducible P_Lac promoter). Our genetic screen and quantitative β-galactosidase assays identified CsrB and its cognate protein CsrA as potential regulators of miaA expression in E. coli. Consistent with our hypothesis that CsrA regulates miaA post-transcriptional gene expression through binding to the miaA mRNA 5′ UTR, and CsrB binds and regulates miaA post-transcriptional gene expression through sequestration of CsrA levels, a deletion of csrA significantly reduced expression of the reporter fusion as well as reducing miaA mRNA levels. These results suggest that under conditions where CsrA is inhibited, miaA mRNA translation and thus MiaA-dependent tRNA modification may be limited. Full article

(This article belongs to the Special Issue Role of RNA Decay in Bacterial Gene Regulation)

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14 pages, 1866 KiB

Open AccessArticle

Naturally Occurring Angiotensin Peptides Enhance the SARS-CoV-2 Spike Protein Binding to Its Receptors

by Katelin X. Oliveira, Fariha E. Bablu, Emily S. Gonzales, Taisuke Izumi and Yuichiro J. Suzuki

Int. J. Mol. Sci. 2025, 26(13), 6067; https://doi.org/10.3390/ijms26136067 - 24 Jun 2025

Abstract

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the virus responsible for Coronavirus Disease 2019 (COVID-19), utilizes its spike protein to infect host cells. In addition to angiotensin-converting enzyme 2 (ACE2) and neuropilin-1 (NRP1), AXL acts as a spike protein receptor and mediates infection, [...] Read more.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the virus responsible for Coronavirus Disease 2019 (COVID-19), utilizes its spike protein to infect host cells. In addition to angiotensin-converting enzyme 2 (ACE2) and neuropilin-1 (NRP1), AXL acts as a spike protein receptor and mediates infection, especially in respiratory cells with low ACE2 expression. Angiotensin II (1–8) can be cleaved into shorter peptides within the biological system. Antibody-based binding assays showed that angiotensin II causes a two-fold increase in the binding between the spike protein and AXL, but not ACE2 or NRP1. While a longer peptide, angiotensin I (1–10), did not affect the spike–AXL binding, shorter lengths of angiotensin peptides exhibited enhancing effects. The C-terminal deletions of angiotensin II to angiotensin (1–7) or angiotensin (1–6) resulted in peptides with enhanced activity toward spike–AXL binding with a similar capacity as angiotensin II. In contrast, the N-terminal deletions of angiotensin II to angiotensin III (2–8) or angiotensin IV (3–8) as well as the N-terminal deletions of angiotensin (1–7) to angiotensin (2–7) or angiotensin (5–7) produced peptides with a more potent ability to enhance spike–AXL binding (2.7-fold increase with angiotensin IV). When valine was substituted for tyrosine at position 4 in angiotensin II or when tyrosine at position 4 was phosphorylated, spike–AXL binding was increased, suggesting that modifications to tyrosine trigger enhancement. Angiotensin IV also enhances spike protein binding to ACE2 and NRP1. Thus, angiotensin peptides may contribute to COVID-19 pathogenesis by enhancing spike protein binding and thus serve as therapeutic targets. Full article

(This article belongs to the Special Issue Advanced Perspectives on Virus–Host Interactions)

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8 pages, 1043 KiB

Open AccessOpinion

PD-L1 Expression in NSCLC: Clouds in a Bright Sky

by Victoria Ferrari, Jocelyn Gal, Baharia Mograbi and Gerard Milano

Int. J. Mol. Sci. 2025, 26(13), 6066; https://doi.org/10.3390/ijms26136066 - 24 Jun 2025

Abstract

Programmed Death-Ligand 1 (PD-L1) is a major target for immunotherapy using checkpoint inhibitors (CPIs), particularly in lung cancer treatment. Tumoral PD-L1 expression has been recognized as a natural predictor of CPI response. This predictive relationship is primarily due to its upregulation by interferon-gamma, [...] Read more.

Programmed Death-Ligand 1 (PD-L1) is a major target for immunotherapy using checkpoint inhibitors (CPIs), particularly in lung cancer treatment. Tumoral PD-L1 expression has been recognized as a natural predictor of CPI response. This predictive relationship is primarily due to its upregulation by interferon-gamma, which is released by immune cells (mainly T lymphocytes and natural killer cells) in proximity to tumor cells, driving an immune resistance mechanism. However, PD-L1 expression is modulated at multiple levels, including oncogenic signaling pathways, and transcriptional and post-transcriptional regulations, potentially leading to false positive predictions. Conversely, variable glycosylation of PD-L1 may compromise the accuracy of immunohistochemical measurements, resulting in false negative predictive data. In addition, PD-L1 expression demonstrates relative instability throughout treatment courses (e.g., chemotherapy and tyrosine kinase inhibitors), further limiting its clinical utility. In this review, we focused on the molecular mechanisms governing PD-L1 expression with a special emphasis on lung cancer. We also discussed biomarker strategies for optimizing patient selection for checkpoint inhibitor therapy where multimodal/multi-omics meta-biomarker approaches are emerging. Such comprehensive PD-L1-enriched biomarker strategies require evaluation through large-scale prospective studies, particularly in lung cancer, where numerous competing predictive candidates exist for CPI response. Full article

(This article belongs to the Special Issue Update on Immunotherapies for Cancer)

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20 pages, 1271 KiB

Open AccessReview

Immunopathology of Antineutrophil Cytoplasmic Antibody (ANCA)-Associated Vasculitis

by Katarzyna Aleksandra Lisowska and Anna Wardowska

Int. J. Mol. Sci. 2025, 26(13), 6065; https://doi.org/10.3390/ijms26136065 - 24 Jun 2025

Abstract

Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) constitutes a group of rare diseases characterized by autoimmune-associated inflammation and vessel damage. Based on the clinical manifestations and involvement of immune components, three disease syndromes are distinguished: granulomatosis with polyangiitis (GPA), microscopic polyangiitis (MPA), and eosinophilic [...] Read more.

Antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) constitutes a group of rare diseases characterized by autoimmune-associated inflammation and vessel damage. Based on the clinical manifestations and involvement of immune components, three disease syndromes are distinguished: granulomatosis with polyangiitis (GPA), microscopic polyangiitis (MPA), and eosinophilic granulomatosis with polyangiitis (EGPA). In this review, we present the current data on the epidemiology, the clinical manifestations of each syndrome, and the most up-to-date classification criteria. The role of the underlying genetic and epigenetic abnormalities, as well as their interplay, is described. The immunological diversification of AAV is also described, with a focus on the immune cell dysfunctions detected in patients. In conclusion, we emphasize the urgent need to unravel the sophisticated mechanisms of this disease, which would enable the development of new, effective therapeutic strategies. Full article

(This article belongs to the Special Issue The Molecular Basis of Vascular Pathology)

37 pages, 1798 KiB

Open AccessReview

Towards Effective Helicobacter pylori Eradication: Emerging Therapies in the Wake of Antibiotic Resistance

by Barathan Muttiah, Wathiqah Wahid, Asif Sukri and Alfizah Hanafiah

Int. J. Mol. Sci. 2025, 26(13), 6064; https://doi.org/10.3390/ijms26136064 - 24 Jun 2025

Abstract

Helicobacter pylori (H. pylori) infection is a leading cause of gastritis, peptic ulcers, and gastric cancer, affecting more than half of the global population. Its persistence in the acidic gastric environment and its ability to evade host immunity present major treatment [...] Read more.

Helicobacter pylori (H. pylori) infection is a leading cause of gastritis, peptic ulcers, and gastric cancer, affecting more than half of the global population. Its persistence in the acidic gastric environment and its ability to evade host immunity present major treatment challenges. Although antibiotics remain the standard therapy, rising antimicrobial resistance has reduced treatment efficacy, prompting the search for alternative and adjunct approaches. Emerging therapies include probiotics, antimicrobial peptides (AMPs), and plant-derived compounds, which target H. pylori through membrane disruption, immunomodulation, or direct antimicrobial activity. Novel drug delivery systems and microbiota-sparing interventions are also being investigated. Additionally, vaccine development offers a promising strategy for long-term protection, though challenges related to antigenic variability and host-specific responses remain. Despite these advances, treatment variability and the limited clinical validation of alternatives hinder progress. A multifaceted approach integrating microbiome research, host–pathogen interactions, and new therapeutic agents is essential for future success. Full article

(This article belongs to the Section Molecular Biology)

23 pages, 17897 KiB

Open AccessArticle

Comparative Analysis of HPA-Axis Dysregulation and Dynamic Molecular Mechanisms in Acute Versus Chronic Social Defeat Stress

by Jiajun Yang, Yifei Jia, Ting Guo, Siqi Zhang, Jin Huang, Huiling Lu, Leyi Li, Jiahao Xu, Gefei Liu and Ke Xiao

Int. J. Mol. Sci. 2025, 26(13), 6063; https://doi.org/10.3390/ijms26136063 - 24 Jun 2025

Abstract

Organisms respond to environmental stress primarily through the autonomic nervous system and hypothalamic–pituitary–adrenal (HPA) axis, regulating metabolism, psychological states, and immune function and modulating memory, reward processing, and immune responses. The HPA axis plays a central role in stress response, exhibiting distinct activation [...] Read more.

Organisms respond to environmental stress primarily through the autonomic nervous system and hypothalamic–pituitary–adrenal (HPA) axis, regulating metabolism, psychological states, and immune function and modulating memory, reward processing, and immune responses. The HPA axis plays a central role in stress response, exhibiting distinct activation patterns under acute versus chronic social defeat stress. However, differences in physiological impacts and regulatory pathways between these stress conditions remain understudied. This study integrates RNA sequencing and behavioral analyses to reveal that acute social defeat stress triggers transient anxiety-like behaviors, accompanied by systemic inflammation and immediate-early gene (IEG) activation. In contrast, chronic social defeat stress induces long-term behavioral and physiological alterations, including neurotransmitter imbalance (e.g., reduced GABA and increased glutamate), sustained activation of maladaptive pathways (e.g., IL-17 signaling), and disrupted corticosterone synthesis. These findings highlight the dynamic regulatory role of the HPA axis under varying stress conditions, providing novel insights into mental health disorders such as anxiety and depression. The study identifies potential therapeutic targets to mitigate chronic social defeat stress effects and offers a theoretical foundation for personalized interventions. Full article

(This article belongs to the Section Molecular Neurobiology)

17 pages, 8884 KiB

Open AccessArticle

Pharmacological Preconditioning with Diazoxide Upregulates HCN4 Channels in Sinoatrial Node of Adult Rat Cardiomyocytes

by Wilibaldo Orea, Elba D. Carrillo, Ascención Hernández, Rubén Moreno, María C. García and Jorge A. Sánchez

Int. J. Mol. Sci. 2025, 26(13), 6062; https://doi.org/10.3390/ijms26136062 - 24 Jun 2025

Abstract

Cardioprotection against ischemia is achieved using openers of mitochondrial ATP-sensitive K⁺ (mitoKATP) channels such as diazoxide (DZX), leading to pharmacological preconditioning (PPC). We previously reported that PPC decreases the abundance of ventricular Cav1.2 channels, but PPC’s effects on other channels remain largely [...] Read more.

Cardioprotection against ischemia is achieved using openers of mitochondrial ATP-sensitive K⁺ (mitoKATP) channels such as diazoxide (DZX), leading to pharmacological preconditioning (PPC). We previously reported that PPC decreases the abundance of ventricular Cav1.2 channels, but PPC’s effects on other channels remain largely unexplored. In this study, we hypothesized that DZX regulates the expression of hyperpolarization-activated cyclic nucleotide potassium channel 4 (HCN4) channels in sinoatrial node cells (SANCs), the specialized cardiomyocytes that generate the heartbeat. DZX increased the heart rate in intact adult rats. Patch-clamp experiments revealed an increase in the magnitude of ionic currents through HCN4 channels, which was abolished by the reactive oxygen species (ROS) scavenger N-acetylcysteine (NAC) and the selective mitoKATP channel inhibitor 5-hydroxydecanoate (5-HD). Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) and Western blot assays showed that DZX increased HCN4 channel expression at the mRNA and protein levels. Immunofluorescence analyses revealed that PPC increased HCN4 fluorescence, which was abolished by NAC. DZX increased nuclear translocation of c-Fos and decreased protein abundance of RE1 silencing transcription factor (REST)/neuron-restrictive silencer factor (NRSF), suggesting the involvement of these factors. Our results suggest that PPC increases the heart rate by upregulating HCN4 channel expression through a mechanism involving c-Fos, REST, and ROS. Full article

(This article belongs to the Special Issue Ion Channels as a Potential Target in Pharmaceutical Designs 2.0)

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27 pages, 1739 KiB

Open AccessReview

The Link Between Dietary Timing and Exercise Performance Through Adipocyte AMPKα2 Signaling

by Sohyun Kim, Jihyun Baek and Man S. Kim

Int. J. Mol. Sci. 2025, 26(13), 6061; https://doi.org/10.3390/ijms26136061 - 24 Jun 2025

Abstract

Emerging evidence suggests that the timing of eating and exercise over the course of the day is paramount to metabolism and physical function. This review highlights seminal studies showing that adipocyte AMPKα2 signaling controls circadian adipose tissue–skeletal muscle communication. Day-restricted feeding has been [...] Read more.

Emerging evidence suggests that the timing of eating and exercise over the course of the day is paramount to metabolism and physical function. This review highlights seminal studies showing that adipocyte AMPKα2 signaling controls circadian adipose tissue–skeletal muscle communication. Day-restricted feeding has been shown to improve exercise performance via adipocyte-specific activation of AMPKα2, which controls fat–muscle crosstalk in a time-of-day dependent manner. This review also discusses corroborating experimental studies designating mesenchymal stem cells as key cellular mediators, showing that exercise in the afternoon leads to better metabolic effects in humans, and illustrating how incorrect timing of food intake leads to leptin resistance and metabolic dysregulation. Multi-omics strategies have shed light on the molecular mechanisms underlying such effects of time, showing the circadian control of metabolic processes across tissues. These results advance our knowledge of chronometabolism and offer exciting temporal intervention treatments for metabolic diseases, such as time-restricted feeding, timed exercise, and chronopharmacological targeting of AMPK. Fat–muscle crosstalk, physical performance, and metabolic health outcomes can possibly be optimized by synchronizing dietary and exercise timing with endogenous circadian rhythms. Full article

(This article belongs to the Special Issue The Role of Protein Kinase in Health and Diseases)

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19 pages, 2617 KiB

Open AccessArticle

A Module-Level Polygenic Risk Score-Based NetWAS Framework for Identifying AD Genetic Modules Mediated by Amygdala: An ADNI Study

by Haoran Luo, Shaoheng Fan, Hongwei Liu, Wei Li, Zhoujie Fan, Xuancheng Zhu, Chen Jason Zhang, Hong Liang, Shan Cong and Xiaohui Yao

Int. J. Mol. Sci. 2025, 26(13), 6060; https://doi.org/10.3390/ijms26136060 - 24 Jun 2025

Abstract

Network-based GWAS (NetWAS) has advanced brain imaging research by identifying genetic modules associated with brain alterations. However, how imaging risk genes exert functions in brain diseases, particularly their mediation through imaging quantitative traits (iQTs), remains underexplored. We propose a module-level polygenic risk score [...] Read more.

Network-based GWAS (NetWAS) has advanced brain imaging research by identifying genetic modules associated with brain alterations. However, how imaging risk genes exert functions in brain diseases, particularly their mediation through imaging quantitative traits (iQTs), remains underexplored. We propose a module-level polygenic risk score (MPRS)-based NetWAS framework to uncover genetic modules associated with Alzheimer’s disease (AD) through the mediation of an iQT, using amygdala density as a case study. Our framework integrates genotype data, brain imaging phenotypes, clinical diagnosis of AD, and protein–protein interaction (PPI) networks to identify AD-relevant modules (ADMs) influenced by iQT-associated genetic variants. Specifically, we conducted a genome-wide association study (GWAS) of amygdala density (

N = 1515

) to identify variants associated with iQT. These variants were mapped onto a PPI network and network propagation was performed to prompt amygdala modules. The meta-GWAS of AD (

N_{1} = 63, 926

;

N_{2} = 455, 267

) was used to calculate MPRS to further identify AD-relevant modules (ADMs). Four modules that showed significant differences in MPRS between AD and controls were identified as ADM. Post-hoc analyses revealed that these ADMs demonstrated strong modularity, showed increased sensitivity to early stages of AD, and significantly mediated the link between ADMs and AD progression through the amygdala. Furthermore, these modules exhibited high tissue specificity within the amygdala and were enriched in AD-related biological pathways. Our MPRS-based framework bridges genetics, intermediate traits, and clinical outcomes and can be adapted for broader biomedical applications. Full article

(This article belongs to the Special Issue New Advances in Research on Alzheimer’s Disease: 2nd Edition)

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17 pages, 2913 KiB

Open AccessArticle

Statistical Optimization of Bacterial Cellulose Production and Its Application for Bacteriophage Immobilization

by Grzegorz Skaradziński, Tomasz Janek, Paulina Śliwka, Aneta Skaradzińska and Wojciech Łaba

Int. J. Mol. Sci. 2025, 26(13), 6059; https://doi.org/10.3390/ijms26136059 - 24 Jun 2025

Abstract

Bacterial cellulose (BC), an extracellular polysaccharide synthesized by various bacterial strains. It exhibits high tensile strength, water retention, crystallinity, and biocompatibility, making it valuable in biomedical, cosmetic, food, textile, and paper industries. This study examined the effects of six carbon sources on BC [...] Read more.

Bacterial cellulose (BC), an extracellular polysaccharide synthesized by various bacterial strains. It exhibits high tensile strength, water retention, crystallinity, and biocompatibility, making it valuable in biomedical, cosmetic, food, textile, and paper industries. This study examined the effects of six carbon sources on BC production by Komagataeibacter sucrofermentans, identifying fructose as the most effective. A Box–Behnken experimental design was employed to investigate the effects of three variables (fructose concentration, temperature, and cultivation time) on cellulose yield. The optimized cultivation conditions were: fructose concentration of 227.5 g/L, temperature of 28.0 °C, and cultivation time of 295 h, resulting in a BC yield of 63.07 ± 2.91 g/L. Subsequently, BC’s potential as a bacteriophage carrier was assessed. Escherichia coli phage T4 and Staphylococcus aureus phage vB_SauS_CS1 (CS1) were immobilized within BC hydrogels, and their antibacterial activities were assessed through in vitro experiments. These findings suggest BC’s promise as a phage delivery platform for biomedical applications. Full article

(This article belongs to the Section Molecular Microbiology)

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4 pages, 165 KiB

Open AccessEditorial

Special Issue “The 25th Anniversary of NO”

by Daniele Mancardi and Michele Samaja

Int. J. Mol. Sci. 2025, 26(13), 6058; https://doi.org/10.3390/ijms26136058 - 24 Jun 2025

Abstract

Nitric oxide (NO), a simple yet remarkably versatile molecule, stands today as a pivotal player in virtually all body systems and cellular compartments [...] Full article

(This article belongs to the Special Issue The 25th Anniversary of NO)

18 pages, 657 KiB

Open AccessReview

Pregnancy and Neonatal Outcomes in Maturity-Onset Diabetes of the Young: A Systematic Review

by Franciszek Ługowski, Julia Babińska, Katarzyna Makowska, Artur Ludwin and Paweł Jan Stanirowski

Int. J. Mol. Sci. 2025, 26(13), 6057; https://doi.org/10.3390/ijms26136057 - 24 Jun 2025

Abstract

Maturity-onset diabetes of the young (MODY)—a monogenic form of diabetes—accounts for approximately 1–2% of all diabetes cases, with GCK-MODY being the second most commonly diagnosed type. Although the inherited nature of the disease implies that the interplay between maternal glycemia and fetal genotype [...] Read more.

Maturity-onset diabetes of the young (MODY)—a monogenic form of diabetes—accounts for approximately 1–2% of all diabetes cases, with GCK-MODY being the second most commonly diagnosed type. Although the inherited nature of the disease implies that the interplay between maternal glycemia and fetal genotype directly influences neonatal outcomes, clinical guidelines for MODY-complicated pregnancies remain underdeveloped. A systematic literature search in the PubMed, Scopus, Web of Science, and Cochrane databases was conducted following the PRISMA guidelines. The study protocol has been logged in the PROSPERO registry with the identification number CRD42024609390. Data, such as MODY type, the gestational age at delivery, mode of delivery, insulin administration, mutational status of the fetus, fetal birthweight (FBW), occurrence of small-/large-for-gestational age fetus, shoulder dystocia, and neonatal hypoglycemia, were extracted and evaluated. Among 19 studies selected for the final analysis, 15 investigated perinatal outcomes in the GCK-MODY variant. Women diagnosed with GCK-MODY treated with insulin delivered approximately 1–2 weeks earlier than those managed with diet alone. FBW was significantly higher in GCK-negative as compared to GCK-positive offspring. Accordingly, fetal macrosomia was notably more common among unaffected neonates. In GCK-affected fetuses, insulin therapy was associated with a significantly lower FBW. Fetal genotype critically modifies perinatal outcomes in GCK-MODY pregnancies. In the absence of fetal genotyping, conservative management should be prioritized to mitigate the risks of fetal growth restriction and iatrogenic prematurity. As data regarding other types of MODY in pregnancy remain sparse, there is an urgent need for more research in this area. Full article

(This article belongs to the Special Issue Gestational Diabetes Mellitus: Molecular Insights into Pathophysiology, Management and Therapy)

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