International Journal of Molecular Sciences

18 pages, 4234 KB

Open AccessArticle

Baicalin Augments 5-Fluorouracil Efficacy in Colorectal Cancer by Triggering MLKL-Dependent Necroptosis: A Novel Strategy to Overcome Chemoresistance

by Jingwen Yuan, Zhiying Peng, Rongbo Wen, Leqi Zhou, Fuao Cao, Tianshuai Zhang, Yingjie Wu, Jiayue Wu, Ran Lin, Guanyu Yu and Wei Zhang

Int. J. Mol. Sci. 2026, 27(6), 2919; https://doi.org/10.3390/ijms27062919 - 23 Mar 2026

Cited by 1 | Viewed by 601

Abstract

5-Fluorouracil (5-Fu) remains essential in colorectal cancer (CRC) treatment, but monotherapy causes severe toxicity and faces chemoresistance. Combination regimens are encouraged to improve efficacy and safety. Natural compounds like Baicalin show anti-tumor potential in other gastrointestinal cancers, yet their role in CRC, particularly [...] Read more.

5-Fluorouracil (5-Fu) remains essential in colorectal cancer (CRC) treatment, but monotherapy causes severe toxicity and faces chemoresistance. Combination regimens are encouraged to improve efficacy and safety. Natural compounds like Baicalin show anti-tumor potential in other gastrointestinal cancers, yet their role in CRC, particularly in overcoming 5-Fu resistance, is underexplored. The combined effect of Baicalin and 5-Fu was evaluated through in vitro functional assays and an in vivo xenograft model. Mechanisms were investigated using Western blot, qPCR, and RNA-seq. Baicalin enhanced 5-Fu to inhibit CRC progression both in vitro and in vivo. Mechanistically, Baicalin enhanced 5-Fu cytotoxicity by activating the MLKL-dependent necroptosis pathway. This study proposes the Baicalin and 5-Fu combination as a novel and potent chemosensitizing strategy for CRC, especially in 5-Fu-resistant cases, and provides a mechanistic rationale for Baicalin as a chemotherapy-enhancing agent. Full article

(This article belongs to the Special Issue Anti-Cancer Drugs: Natural Products, Synthetic Compounds and Potential Pharmacological Effects and Applications)

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23 pages, 3593 KB

Open AccessArticle

A Study on the Mechanism of Acetyl Tributyl Citrate-Induced Infertility Toxicity and the Protective Action of Icariin Based on Network Toxicology, Network Pharmacology, Molecular-Docking Technology and Molecular Dynamics Simulation

by Xiaowei Sun, Peng Chen, Yuxing Han, Yuqing Du, Siyu Sun, Jin Miu, Xueying Li, Shaobo Liu and Chunlei Wan

Int. J. Mol. Sci. 2026, 27(6), 2918; https://doi.org/10.3390/ijms27062918 - 23 Mar 2026

Viewed by 882

Abstract

Infertility is a prevalent clinical issue which disrupts normal human life and exerts an impact on fertility rates within the population. The increase in environmental pollutants, including acetyl tributyl citrate (ATBC), has given rise to concerns regarding their potential toxicity in infertility-related disorders. [...] Read more.

Infertility is a prevalent clinical issue which disrupts normal human life and exerts an impact on fertility rates within the population. The increase in environmental pollutants, including acetyl tributyl citrate (ATBC), has given rise to concerns regarding their potential toxicity in infertility-related disorders. Icariin exhibits therapeutic effects on infertility, yet its mechanism of action against plasticiser-induced reproductive disorders remains unclear. This study aims to elucidate the potential toxicological targets and molecular mechanisms of ATBC-induced infertility, as well as the therapeutic targets and mechanisms of icariin in treating ATBC-induced reproductive disorders, through network toxicology, molecular-docking techniques and molecular dynamics simulation. Utilising the component-target database SwissTargetPrediction, the Similarity Ensemble Approach, PharmMapper, the ChEMBL database, and disease databases including the Therapeutic Target Database, OMIM, GeneCards, and DrugBank, 63 targets for ATBC-induced infertility and 33 targets for icariin treatment were identified. Screening via the STRING platform and Cytoscape 3.10.1 software yielded four core targets for ATBC-induced infertility—HSP90AA1, PIK3CA, CASP3, HRAS—and four core targets for icariin treatment—IL6, TNF, STAT3, and INS. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that ATBC-induced infertility correlates with pathways including pathways in cancer, prostate cancer, and PI3K-Akt signalling pathways. Conversely, the core targets of icariin therapy for related reproductive disorders are closely associated with tumour-associated signalling pathways and the AGE-RAGE signalling pathway. Molecular-docking and molecular dynamics simulation further confirmed the strong binding interactions between ATBC and infertility-related targets, as well as between icariin and core targets for treating reproductive disorders. This provides a theoretical foundation for understanding ATBC’s toxicological targets and the complex molecular mechanisms underpinning icariin’s treatment of infertility. It informs the development of strategies for icariin to prevent and treat infertility caused by exposure to ATBC-containing plastics or excessive ATBC contact. Full article

(This article belongs to the Section Molecular Toxicology)

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13 pages, 7389 KB

Open AccessArticle

PPARγ Mediates Transdifferentiation of CX3CR1⁺-Derived Cells into Adipocytes

by Yong-Feng Yang, Cheng-Chao Ruan and Yu Lei

Int. J. Mol. Sci. 2026, 27(6), 2917; https://doi.org/10.3390/ijms27062917 - 23 Mar 2026

Viewed by 463

Abstract

Transdifferentiation of one cell type into another occurs under normal physiological conditions. Adipose tissue is an important metabolic and endocrine organ involved in the onset and progression of various diseases. Previous studies have shown that fibroblasts can transdifferentiate into adipocytes. Here, we demonstrate [...] Read more.

Transdifferentiation of one cell type into another occurs under normal physiological conditions. Adipose tissue is an important metabolic and endocrine organ involved in the onset and progression of various diseases. Previous studies have shown that fibroblasts can transdifferentiate into adipocytes. Here, we demonstrate that CX3CR1-derived cells can also transdifferentiate into adipocytes. Additionally, RFP⁺ SVF cells and mature adipocytes were identified in different adipose tissues of Cx3cr1^cre: Rosa26^Td mice. Cold exposure enhances the adipogenic transdifferentiation of RFP⁺ cells, whereas a high-fat diet (HFD) inhibits this process. Mechanistically, we found that PPARγ regulates transdifferentiation, suggesting its role in the differentiation of CX3CR1-derived cells into adipocytes, thus offering new insights into the origin of adipocytes in the body. Full article

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

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24 pages, 2688 KB

Open AccessArticle

Ligand-Dependent and -Independent Functions of Activation Function 1 of Progesterone Receptor in Genome-Wide Gene Regulation and in Cell Proliferation and Apoptosis of Breast Cancer Cells

by Pheck Khee Lau, Bernett Lee Teck Kwong, Shi Hao Lee, Chew Leng Lim, Qian Yee Woo, Amanda Rui En Woo, Jace Koh and Valerie C. L. Lin

Int. J. Mol. Sci. 2026, 27(6), 2916; https://doi.org/10.3390/ijms27062916 - 23 Mar 2026

Viewed by 629

Abstract

Progesterone receptor (PR) regulates gene expression through recruiting coregulators and general transcription factors by activation functions AF1 and AF2. AF1 localizes to the non-conserved and disordered N-terminal domain and is believed to facilitate tissue- and gene-specific activity. Our previous proteomic analysis identified three [...] Read more.

Progesterone receptor (PR) regulates gene expression through recruiting coregulators and general transcription factors by activation functions AF1 and AF2. AF1 localizes to the non-conserved and disordered N-terminal domain and is believed to facilitate tissue- and gene-specific activity. Our previous proteomic analysis identified three key residues (K464, K481 and R492) in AF1 that are monomethylated. Methylation mimic mutations KKR → FFF created hypoactive PR, whereas the KKR → QQQ mutation generated hyperactive PR in gene reporter assays. The current study used these mutants to determine the roles of AF1 in PR regulation of cellular activities and global gene regulation in breast cancer cells MCF-7. AF1-FFF mutation attenuated PR regulation of cell proliferation and apoptosis in response to progestin, whereas AF1-QQQ mutation enhanced these effects. AF1-FFF mutation attenuated gene regulation by progestin in ~60% of PR target genes, including genes involved in cell proliferation, hypoxia and TNFα signaling. However, the AF1-FFF mutation had little effect on ligand-independent gene regulation, suggesting distinct mechanisms of gene regulation by liganded and unliganded PR. Intriguingly, impaired activity of methylation mimic mutant PRB-FFF is associated with greater chromatin binding in ChIP-Seq analysis, corresponding to a stronger association between PRB-FFF and Steroid Receptor Coactivator-1 (SRC-1), a member of the p160 family of nuclear receptor coactivators, as was previously reported. In conclusion, PR AF1 is important for the core activities of liganded PR in regulating ~half of target genes and cell proliferation. AF1 monomethylation may modulate PR-chromatin interactions through stronger association with coregulators, thereby decelerating chromatin binding kinetics. This is supported by PRODIGY’s prediction of higher binding affinities of monomethylated AF1 and methylation mimic mutant with SRC-1. Full article

(This article belongs to the Special Issue New Insights into the Structure and Function of Nuclear Receptors)

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20 pages, 3151 KB

Open AccessArticle

Functional siRNA Delivery via Jet Nebulization: Proof-of-Concept IL-1ß Silencing in Macrophage-like THP-1 Cells

by Duy Bao Tran Nguyen, Ahmed S. M. Ali, Dongwei Wu, Johanna Berg, Daniel C. Lauster, Jens Kurreck and Beatrice Tolksdorf

Int. J. Mol. Sci. 2026, 27(6), 2915; https://doi.org/10.3390/ijms27062915 - 23 Mar 2026

Viewed by 625

Abstract

The efficient delivery of small interfering RNAs (siRNAs) to immune and respiratory cells represents a key methodological challenge in developing inhaled RNA interference (RNAi) approaches. A central question is whether siRNA functionality is preserved following aerosolization, as the mechanical stress of nebulization may [...] Read more.

The efficient delivery of small interfering RNAs (siRNAs) to immune and respiratory cells represents a key methodological challenge in developing inhaled RNA interference (RNAi) approaches. A central question is whether siRNA functionality is preserved following aerosolization, as the mechanical stress of nebulization may compromise siRNA integrity and silencing activity. Here, we report a proof-of-concept study using THP-1-derived macrophage-like cells as a tractable in vitro model to characterize jet nebulization for siRNA delivery. Three siRNA candidates targeting interleukin-1 beta (IL-1β) were computationally designed and validated for potent silencing activity and low cytotoxicity. Using a commercially available, off-the-shelf jet nebulizer combined with Lipofectamine RNAiMAX, we demonstrate that siRNA-lipoplexes retain their gene-silencing activity after aerosolization, achieving robust IL-1β knockdown. The delivery efficiency was influenced by siRNA-lipoplex complexation, highlighting the importance of formulation parameters. These findings establish a practical and accessible in vitro platform for evaluating nebulized siRNA functionality, providing a foundation for future studies in more complex and physiologically relevant airway models. Full article

(This article belongs to the Special Issue Recent Advances in RNA Drug Development)

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30 pages, 11413 KB

Open AccessArticle

Bumped Kinase Inhibitor BKI-1708 Interferes in Cytokinesis and Drives Baryzoite Conversion in the Cyst-Forming Apicomplexan Parasites Toxoplasma gondii, Neospora caninum and Besnoitia besnoiti

by Maria Cristina Ferreira de Sousa, Joachim Müller, Kai Pascal Alexander Hänggeli, Manfred Heller, Anne-Christine Uldry, Sophie Braga-Lagache, Alexandre Leitao, Luis-Miguel Ortega-Mora, Kayode K. Ojo, Wesley C. Van Voorhis and Andrew Hemphill

Int. J. Mol. Sci. 2026, 27(6), 2914; https://doi.org/10.3390/ijms27062914 - 23 Mar 2026

Viewed by 697

Abstract

Bumped kinase inhibitors (BKIs) have demonstrated safety and promising efficacy against various apicomplexan pathogens both in vitro and in vivo, but do not act parasiticidal in vitro. In the closely related cyst-forming coccidians Toxoplasma gondii, Neospora caninum and Besnoitia besnoiti, treatments [...] Read more.

Bumped kinase inhibitors (BKIs) have demonstrated safety and promising efficacy against various apicomplexan pathogens both in vitro and in vivo, but do not act parasiticidal in vitro. In the closely related cyst-forming coccidians Toxoplasma gondii, Neospora caninum and Besnoitia besnoiti, treatments with BKI-1708 induce the conversion of intracellular tachyzoites into atypical multinucleated complexes named “baryzoites”. In this study, we comparatively assessed tachyzoites and baryzoites of all three species with respect to ultrastructure, differential antigen expression by immunofluorescence, and overall differential protein expression by MS-proteomics. TEM demonstrated common, but also distinguishing, structural features in baryzoites of the three species. They contained newly formed zoites, unable to complete cytokinesis, and thus they were trapped intracellularly. An electron-dense cyst wall-like structure was found only in T. gondii baryzoites. Species-specific differences in antigen expression were observed by immunofluorescence. Comparative proteomic analysis of baryzoites versus tachyzoites revealed a downregulation of ribosomal proteins, proteins associated with secretory organelles, as well as of transcription and translation factors in baryzoites across all species. Bradyzoite-specific markers were upregulated only in T. gondii baryzoites. Two alveolin-domain filament proteins and a hypothetical protein (TGME49_236950, NCLIV_050850, BESB_060040) were detected at higher abundance in all three species. Thus, baryzoites exhibit distinct phenotypic and proteomic profiles, with ambiguous expression of tachyzoite and bradyzoite antigens, suggesting a reversible response to stress rather than progression into a fully differentiated form. Full article

(This article belongs to the Section Molecular Microbiology)

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17 pages, 608 KB

Open AccessReview

The Heart–Gut Axis in Heart Failure: The Role of Next-Generation Pharmacological Therapies

by Elia Nunzio Maria Salerno, Isabella Fumarulo, Claudia Mendicino, Marcello Vaccarella, Barbara Garramone, Francesco Gallo, Gerardo Volzone, Andrea Cammuso, Vincenzo Della Candelora, Franco Scaldaferri, Loris Riccardo Lopetuso, Antonio Gasbarrini, Francesco Burzotta and Nadia Aspromonte

Int. J. Mol. Sci. 2026, 27(6), 2913; https://doi.org/10.3390/ijms27062913 - 23 Mar 2026

Viewed by 775

Abstract

Heart failure (HF) is a systemic syndrome in which cardiac dysfunction is closely linked to multiorgan involvement, including the gastrointestinal tract. Increasing evidence highlights the relevance of the gut–heart axis in HF pathophysiology, whereby intestinal hypoperfusion, congestion, and barrier dysfunction promote gut microbiota [...] Read more.

Heart failure (HF) is a systemic syndrome in which cardiac dysfunction is closely linked to multiorgan involvement, including the gastrointestinal tract. Increasing evidence highlights the relevance of the gut–heart axis in HF pathophysiology, whereby intestinal hypoperfusion, congestion, and barrier dysfunction promote gut microbiota dysbiosis, systemic inflammation, and adverse cardiovascular outcomes. In parallel, the advent of novel HF therapies, particularly sodium–glucose cotransporter 2 inhibitors (SGLT2i) and the angiotensin receptor–neprilysin inhibitor sacubitril/valsartan, has markedly improved clinical outcomes across HF phenotypes. Beyond their established cardiovascular benefits, these therapies may exert pleiotropic effects that extend to the intestinal environment and the gut microbiota. Through integrated actions on hemodynamics, neurohormonal activation, metabolic pathways, and inflammatory processes, recent data suggest that novel HF drugs may indirectly influence the gut-microbial composition and function. Conversely, the gut microbiota may modulate drug efficacy and result in interindividual variability in therapeutic responses, suggesting a bidirectional interaction between pharmacological treatment and the gut ecosystem. This narrative review summarizes current evidence of gut microbiota alterations in HF and critically examines emerging data on interactions between the gut microbiota and novel HF therapies, focusing on SGLT2 inhibitors and sacubitril/valsartan. Understanding this crosstalk may support the development of microbiota-informed, personalized therapeutic strategies in heart failure. Full article

(This article belongs to the Special Issue Advanced Molecular Research in Cardiology and Treatment Approaches)

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17 pages, 4795 KB

Open AccessArticle

Identification and Expression Analysis of the Goji Haploid-Inducible Gene DMP

by Zijun Yang, Cuiping Wang, Zhonghua Wang and Jiali Wu

Int. J. Mol. Sci. 2026, 27(6), 2912; https://doi.org/10.3390/ijms27062912 - 23 Mar 2026

Viewed by 435

Abstract

Goji, a plant unique to China, is recognized for its dual use as both a food and a medicine and is rich in various nutrients. However, long-term asexual propagation often leads to cultivar degeneration and viral accumulation, which severely impact its yield, quality, [...] Read more.

Goji, a plant unique to China, is recognized for its dual use as both a food and a medicine and is rich in various nutrients. However, long-term asexual propagation often leads to cultivar degeneration and viral accumulation, which severely impact its yield, quality, and disease resistance. Homozygous seeds can stably produce offspring with uniform traits. Haploid breeding technology, which involves doubling the chromosomes of haploid plants to obtain homozygous diploids, can significantly accelerate the breeding process. The DMP (Domain of Unknown Function 679 Membrane Protein) family is a plant-specific family of membrane proteins involved in various biological functions, including physiological processes, reproductive development, and senescence. Concurrently, loss-of-function of the DMP gene impedes the proper integration of the paternal genome following fertilization. Consequently, the embryo develops with exclusively maternal chromosomes, a mechanism that underlies the induction of haploids. In this study, we conducted a genome-wide identification of the DMP gene family in goji, analyzing the physicochemical properties, chromosomal locations, cis-acting elements, phylogenetic relationships, sequence characteristics, expression patterns, and subcellular localization of its members. The objective was to identify DMP genes capable of inducing haploid production in goji berry for future breeding applications. The results revealed a total of 11 DMP family members in the goji berry genome, distributed across seven chromosomes. The proteins encoded by these members contain 136 to 237 amino acids, with molecular weights ranging from 15,267.96 to 26,141.01 Da and isoelectric points (pI) ranging from 5.14 to 9.32. The LbDMPs were found to contain numerous cis-acting elements that play roles in plant responses to abiotic stresses and various phytohormones. Notably, LbDMP1 and LbDMP11, which contain the typical DUF679 domain, are predominantly expressed in pollen, suggesting their involvement in the reproductive process of goji berry. They were therefore identified as candidate genes for haploid induction. Subcellular localization analysis demonstrated that LbDMP1 is localized to the plasma membrane, while LbDMP11 is localized to membrane systems such as the endoplasmic reticulum. This research provides a fundamental basis for further exploration of the functional roles of the DMP gene family in goji berry and offers valuable genetic resources for haploid induction in its breeding programs. Full article

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

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19 pages, 7343 KB

Open AccessArticle

Galactokinase 1 Inhibition-Induced Cell Cycle Arrest and Apoptosis in Bladder Cancer Cells Is Associated with AKT Signaling Downregulation

by Surya P. Singh, Ronghao Liu, Feng Yan, Qinggong Tang, Chinthalapally V. Rao and Venkateshwar Madka

Int. J. Mol. Sci. 2026, 27(6), 2911; https://doi.org/10.3390/ijms27062911 - 23 Mar 2026

Viewed by 682

Abstract

Bladder cancer (BCa) is the second most common cancer of the genitourinary tract globally. It has limited treatment options, high recurrence rate, and acquires resistance to platinum-based therapy. Therefore, identifying novel therapeutic targets is urgently needed. Analysis of the TCGA data revealed that [...] Read more.

Bladder cancer (BCa) is the second most common cancer of the genitourinary tract globally. It has limited treatment options, high recurrence rate, and acquires resistance to platinum-based therapy. Therefore, identifying novel therapeutic targets is urgently needed. Analysis of the TCGA data revealed that the enzyme galactokinase-1 (GALK1) is overexpressed (p < 0.0001) in bladder tumors compared to normal tissue. Our data also confirmed GALK1 protein upregulation in multiple human BCa cell lines and rodent bladder tumors. However, the precise role of GALK1 in BCa progression and effects of its specific inhibitor remain unexamined. In this study, we demonstrate that GALK1 gene silencing using shRNA resulted in a significant reduction in BCa cell proliferation, migration, and invasion. Pharmacological inhibition of GALK1 using small molecule Cpd36 resulted in anticancer efficacy against BCa. Cpd36 inhibited proliferation, migration, and invasion of BCa cells. Further, Cpd36 induced G1 phase cell cycle arrest, apoptosis, mitochondrial membrane depolarization, and ROS production in the BCa cells. Mechanistically, Cpd36-induced reduction in cell proliferation was associated with a decrease in expression of GALK1, PCNA proteins. Inhibition of metastatic potential was accompanied by decreased migration, invasion, and MMP-9 expression. Cell cycle arrest was associated with decrease in Cyclin D1 and increased expression of p21 and p27. Induction of apoptosis was linked with increased expression of cleaved caspase-3 and cleaved PARP, while downregulating p-AKT. Additionally, Cpd36 in combination with cisplatin or gemcitabine showed a strong synergistic effect on BCa cells. Taken together, our findings suggest that GALK1 plays a significant role in BCa cell survival and validates its inhibitors as promising therapeutic options for managing this disease. Full article

(This article belongs to the Special Issue Molecular Diagnostic and Treatment Methods in Socially Significant Diseases in Urology)

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17 pages, 678 KB

Open AccessReview

Physiological Implications of Pancreatic Amyloid Polypeptide Aggregation and Its Inhibition by Melatonin

by Yeong-Min Yoo and Seong Soo Joo

Int. J. Mol. Sci. 2026, 27(6), 2910; https://doi.org/10.3390/ijms27062910 - 23 Mar 2026

Viewed by 511

Abstract

Type 2 Diabetes (T2D) is characterized by the toxic aggregation of human islet amyloid polypeptide (hIAPP or amylin) within pancreatic β-cells. IAPP is also a neuropancreatic hormone that plays a significant role in Alzheimer’s disease (AD) by co-depositing with amyloid-beta (Aβ) and Tau, [...] Read more.

Type 2 Diabetes (T2D) is characterized by the toxic aggregation of human islet amyloid polypeptide (hIAPP or amylin) within pancreatic β-cells. IAPP is also a neuropancreatic hormone that plays a significant role in Alzheimer’s disease (AD) by co-depositing with amyloid-beta (Aβ) and Tau, supporting the Type 3 Diabetes (T3D) hypothesis. Soluble IAPP accelerates Aβ aggregation through cross-seeding and causes neurotoxicity by impairing the blood–brain barrier and activating neuroinflammation. Melatonin inhibits these processes by disrupting hydrophobic interactions in both hIAPP and Aβ, preventing the formation of toxic β-sheet structures. Furthermore, melatonin promotes amyloid clearance via the glymphatic and lymphatic systems, protects neurons from oxidative damage, and reduces Tau hyperphosphorylation. This suggests that melatonin serves as a promising multitarget therapeutic agent for both metabolic and neurodegenerative disorders by modulating structural protein transformations. Full article

(This article belongs to the Special Issue Advances in Amyloid Aggregation and Its Inhibition: Implementing Insights from Physiological Conditions)

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24 pages, 23493 KB

Open AccessArticle

Pancancer Analysis and the Oncogenic Role of UBTF in Breast Invasive Carcinoma

by Mingang He, Yi Wu, Simeng Liu, Yifeng Hou, Hefen Sun and Wei Jin

Int. J. Mol. Sci. 2026, 27(6), 2909; https://doi.org/10.3390/ijms27062909 - 23 Mar 2026

Viewed by 552

Abstract

Upstream binding transcription factor (UBTF) is a nuclear transcription factor implicated in ribosome biogenesis, yet its pancancer relevance and immunological associations remain incompletely understood. We integrated datasets from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Human Protein Atlas (HPA), Cancer [...] Read more.

Upstream binding transcription factor (UBTF) is a nuclear transcription factor implicated in ribosome biogenesis, yet its pancancer relevance and immunological associations remain incompletely understood. We integrated datasets from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Human Protein Atlas (HPA), Cancer Cell Line Encyclopedia (CCLE), and cBioPortal databases to characterize UBTF expression, genomic alterations, and prognostic value across 33 cancer types. Immune microenvironment analyses were performed using ESTIMATE and multiple deconvolution algorithms. CRISPR-Cas9–mediated UBTF depletion was conducted in breast invasive carcinoma (BRCA) cell lines to evaluate functional roles. UBTF was broadly upregulated in multiple tumors with recurrent copy number gains. Survival analyses revealed cancer type–dependent prognostic associations. UBTF expression correlated with immune/stromal contexture, checkpoint features, and predicted immunotherapy response. In BRCA, UBTF depletion reduced proliferation and migration while increasing apoptosis. A UBTF-related prognostic signature effectively stratified patient outcomes and was associated with immune infiltration and predicted immunotherapy response. UBTF represents a pancancer biomarker linked to tumor immunity, with validated functional significance in BRCA and potential utility for risk stratification. Full article

(This article belongs to the Special Issue Molecular Research and Immune Landscape of Breast Cancer)

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27 pages, 4653 KB

Open AccessArticle

Pyridinium-Fused 1,3-Selenazoles via Cyclizations of 2-Pyridylselenyl Chloride with Alkynes: Synthesis, Structures, and Antifungal Properties

by Evgeny A. Dukhnovsky, Alexey S. Kubasov, Olga G. Chusova, Victor N. Khrustalev, Alexander V. Borisov, Francis Verpoort, Rosa M. Gomila, Antonio Frontera, Zhishen Ge and Alexander G. Tskhovrebov

Int. J. Mol. Sci. 2026, 27(6), 2908; https://doi.org/10.3390/ijms27062908 - 23 Mar 2026

Viewed by 454

Abstract

We report a straightforward and versatile synthetic route to pyridinium-fused 1,3-selenazoles via the electrophilic cyclization of 2-pyridylselenyl chloride with alkynes. The reaction proceeds efficiently under mild conditions with representative terminal and internal alkynes. While the cyclization exhibits high regioselectivity favoring the 3-substituted isomer [...] Read more.

We report a straightforward and versatile synthetic route to pyridinium-fused 1,3-selenazoles via the electrophilic cyclization of 2-pyridylselenyl chloride with alkynes. The reaction proceeds efficiently under mild conditions with representative terminal and internal alkynes. While the cyclization exhibits high regioselectivity favoring the 3-substituted isomer for most substrates, reactions with 2-pyridyl- and 2-quinolylacetylenes yield regioisomeric mixtures. DFT calculations rationalize this divergence, revealing a competition between kinetic and thermodynamic control; the 3-isomer is kinetically favored, while the 2-isomer is thermodynamically stabilized by an ancillary chalcogen bond between the selenium atom and the pyridine nitrogen of the alkyne substituent. Molecular structures were confirmed by single-crystal X-ray diffraction, and the non-covalent interactions governing supramolecular assembly in the solid state were rigorously analyzed using MEP surfaces, the QTAIM, and NBO analysis. Antifungal evaluation identified several compounds with notable activity against phytopathogenic fungi, highlighting the potential of this novel heterocyclic scaffold in agrochemical applications. Full article

(This article belongs to the Special Issue Editorial Board Members’ Collection Series: “Selenium and Sulfur Chemistry”)

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24 pages, 4341 KB

Open AccessArticle

Bioprospecting of Aerobic Bacteria with Proteolytic Potential Isolated from Animal and Water Sources in the Three Regions of Mainland Ecuador

by Karla Garcés, Juan Manuel Cevallos, Alisson Sisa, Ana Belén Encalada, Oscar Martínez-Álvarez and Mauricio Mosquera

Int. J. Mol. Sci. 2026, 27(6), 2907; https://doi.org/10.3390/ijms27062907 - 23 Mar 2026

Viewed by 509

Abstract

The growing demand for efficient and cost-effective industrial proteases has intensified bioprospecting efforts in diverse ecosystems as a strategy to identify microorganisms with enhanced enzymatic performance. This study aimed to isolate, identify, and evaluate aerobic protease-producing bacteria from animal-protein matrices and water sources [...] Read more.

The growing demand for efficient and cost-effective industrial proteases has intensified bioprospecting efforts in diverse ecosystems as a strategy to identify microorganisms with enhanced enzymatic performance. This study aimed to isolate, identify, and evaluate aerobic protease-producing bacteria from animal-protein matrices and water sources collected across the three continental regions of Ecuador, and to assess their suitability for industrial enzyme production A total of 34 bacterial strains were isolated and taxonomically assigned to the orders Enterobacterales, Pseudomonadales, and Bacillales. Proteolytic activity was evaluated using azocasein and casein assays after cultivation in an optimized medium containing 1% soybean paste as an inducer at 37 °C and 120 rpm for 72 h. Enterobacter cloacae (BC, pork), Bacillus paramycoides (P2, snook), and Pseudomonas aeruginosa (CH1, chontacuro) were identified as the most active protease producers from the Andean (Sierra), coastal (Costa), and Amazon regions, respectively. Production kinetics revealed marked strain-dependent differences. BC and P2 reached maximum proteolytic activity on day 4 followed by a decline, whereas CH1 peaked on day 2 and maintained stable activity over time, indicating superior enzymatic stability. Partial purification by gel-filtration chromatography (Sephadex G-100) yielded fractions with enhanced proteolytic activity, while SDS-PAGE analysis confirmed successful enrichment of protease-containing fractions. Overall, the results demonstrate that ecological origin strongly influences protease production and stability, and identify Pseudomonas aeruginosa CH1 as a particularly promising candidate for industrial applications requiring robust and sustained proteolytic activity. Full article

(This article belongs to the Special Issue Microbial Enzymes for Biotechnological Applications: 2nd Edition)

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16 pages, 4877 KB

Open AccessArticle

A Study on the Stability and Carbohydrate Metabolic Traits of Starter Cultures in Response to Continuous Subculturing

by Yangyang Yu, Jianjun Yang, Ran Wang, Lele Zhang, Kai Zhou, Baolei Li, Baochao Hou, Yue Sang, Haihong Feng, Yan Zhang, Jian He and Xiaoxia Li

Int. J. Mol. Sci. 2026, 27(6), 2906; https://doi.org/10.3390/ijms27062906 - 23 Mar 2026

Viewed by 401

Abstract

The industrial application of starter cultures requires stable physiological and genetic performance. In this study, Streptococcus salivarius subsp. thermophilus and Lactobacillus delbrueckii subsp. bulgaricus were continuously subcultured. Physiological stability was assessed through colony morphology, fermentation activity, and growth profiling. Genetic stability was evaluated [...] Read more.

The industrial application of starter cultures requires stable physiological and genetic performance. In this study, Streptococcus salivarius subsp. thermophilus and Lactobacillus delbrueckii subsp. bulgaricus were continuously subcultured. Physiological stability was assessed through colony morphology, fermentation activity, and growth profiling. Genetic stability was evaluated through comparative genomics of carbohydrate metabolism networks and single-nucleotide polymorphism (SNP) analysis. The results showed that after 2000 generations, the cellular morphology of the strains remained intact. Additionally, the strains exhibited enhanced growth performance and fermentation capability. The Gompertz model revealed that adapted S. thermophilus A37 and L. bulgaricus B29 exhibited shortened lag phases, increased maximum specific growth rates, and high stationary-phase cell densities. Phenotypic microarray and comparative genomics revealed that S. thermophilus mainly used mono- and disaccharides, with impaired ribose metabolism due to the absence of the rbsk gene in the pentose phosphate pathway. In contrast, L. bulgaricus metabolized diverse oligosaccharides, sugar alcohols, and plant-derived substrates. Additionally, it effectively catabolized ribose through the phosphoketolase pathway and possessed a trehalose degradation cluster. All strains exhibited genomic stability, with SNPs revealing fewer than 21 variations per isolate. This study provides an important theoretical foundation for evaluating the stability of fermentation starter cultures. Full article

(This article belongs to the Special Issue Microbial Metabolism: From Pathway Analysis to Metabolic Engineering and Synthetic Biology)

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30 pages, 11565 KB

Open AccessArticle

Exploring the Role of GGA2 in Cancer Progression: Pan-Cancer Bioinformatics and Experimental Validation in Prostate Cancer

by Yangyang Han, Ziyu Huang, Yuxuan Zou, Yunbo Zhang, Huizhen Xin, Meng Sun, Yimin Liu, Mengqi Zhang and Mengjia Li

Int. J. Mol. Sci. 2026, 27(6), 2905; https://doi.org/10.3390/ijms27062905 - 23 Mar 2026

Viewed by 449

Abstract

Cancer remains a significant challenge to global public health. Preliminary studies indicate that the protein Golgi-associated, Gamma-adaptin Ear Containing, ARF Binding Protein 2 (GGA2) may influence various cancers. However, the potential role of GGA2 in oncogenesis remains unknown. We utilized data from The [...] Read more.

Cancer remains a significant challenge to global public health. Preliminary studies indicate that the protein Golgi-associated, Gamma-adaptin Ear Containing, ARF Binding Protein 2 (GGA2) may influence various cancers. However, the potential role of GGA2 in oncogenesis remains unknown. We utilized data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) projects to analyze GGA2 expression levels. Genetic variations and protein expression of GGA2 in human tissues were assessed using the cBioPortal. Gene Set Enrichment Analysis (GSEA) provided deeper insights into GGA2’s oncogenic functions. Comprehensive analysis of TCGA datasets combined with ESTIMATE and TIMER tools demonstrated significant correlations between GGA2 expression levels and clinical outcomes, survival metrics, genomic instability markers (microsatellite instability (MSI)/tumor mutational burden (TMB)), and immune microenvironment composition. Functional validation in prostate cancer models employed qRT-PCR quantification, immunoblotting verification, and cellular behavior assessments through colony formation, Transwell migration, and wound closure assays. Our findings suggest GGA2 could serve as a prognostic biomarker in various cancers. Abnormal levels of GGA2 promoter methylation and genetic alterations may contribute to its dysregulated expression in some cancers. Distinctly, GGA2 expression correlates with MSI and TMB across different cancers and is linked to the expression of immune checkpoint genes. Functionally, GGA2 is instrumental in inhibiting oncogenic mechanisms by diminishing the proliferation, colony formation, invasion, and migratory capabilities of prostate cancer cells. Our study shows that the oncogenic role of GGA2 in various cancers and GGA2 could be served as a biomarker of PARD. Full article

(This article belongs to the Section Molecular Oncology)

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21 pages, 2068 KB

Open AccessReview

Understanding the qPCR Standard Curve: From Assay Validation to Absolute Quantification and Variance PCR

by Mikael Kubista, Amin Forootan, Michael W. Pfaffl, Stephen A. Bustin, Jose M. Andrade, Robert Sjöback, Björn Sjögreen and Anders Ståhlberg

Int. J. Mol. Sci. 2026, 27(6), 2904; https://doi.org/10.3390/ijms27062904 - 23 Mar 2026

Viewed by 1908

Abstract

The quantitative polymerase chain reaction (PCR) standard curve is the central analytical tool for validating qPCR assays and can also be used to estimate target concentrations in test samples. This review explains how qPCR standard curves are constructed, validated, and analyzed for different [...] Read more.

The quantitative polymerase chain reaction (PCR) standard curve is the central analytical tool for validating qPCR assays and can also be used to estimate target concentrations in test samples. This review explains how qPCR standard curves are constructed, validated, and analyzed for different purposes. We first examine an idealized standard curve generated using an exceptionally high number of replicates, far exceeding typical routine use. This approach clearly illustrates fundamental qPCR characteristics and provides an educational framework for defining and estimating PCR efficiency, limit of detection, and limit of quantification. Furthermore, we demonstrate that, in theory, variation in threshold crossing points across replicates can be used to estimate the number of target molecules in a sample. This method, which we term variance PCR, could complement digital PCR and potentially extend the dynamic range of absolute quantification. We also analyze a representative standard curve as typically processed in routine qPCR workflows. This includes validating its dynamic range, assessing the impact of outliers, estimating PCR efficiency and precision, and finally applying the curve to determine the concentration of test samples. Full article

(This article belongs to the Special Issue 25th Anniversary of IJMS: Updates and Advances in Molecular Pathology, Diagnostics, and Therapeutics)

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14 pages, 914 KB

Open AccessArticle

Molecular Investigation of Eimeria spp. Infection in Weaned Dairy Calves in Thessaly, Greece, and Associated Risk Factors

by Konstantinos V. Arsenopoulos, Sotiris Chrysanthopoulos and Elias Papadopoulos

Int. J. Mol. Sci. 2026, 27(6), 2903; https://doi.org/10.3390/ijms27062903 - 23 Mar 2026

Viewed by 517

Abstract

This study presents the first molecular investigation into the prevalence and risk factors of Eimeria spp. infection among weaned dairy calves in Thessaly, Greece. Utilizing a cross-sectional design, 665 fecal samples were collected from 35 intensive dairy cattle farms and analyzed via genus-specific [...] Read more.

This study presents the first molecular investigation into the prevalence and risk factors of Eimeria spp. infection among weaned dairy calves in Thessaly, Greece. Utilizing a cross-sectional design, 665 fecal samples were collected from 35 intensive dairy cattle farms and analyzed via genus-specific PCR and species-specific multiplex PCR targeting the internal transcribed spacer 1 (ITS-1) region. The overall molecular prevalence was found to be 46.3%, with Eimeria bovis (24.7%) and Eimeria zuernii (14.0%) emerging as the most prevalent species. Mixed infections were common, occurring in 51.0% of the positive cases. Multivariable analysis revealed that dairy calves aged less than 60 days had 2.15 times higher odds of infection compared to older calves. Environmental factors also significantly influenced infection rates, specifically ground flooring, the use of immovable/concrete water troughs and infrequent cleaning of floors, feeders and water troughs. These results highlight the high burden of pathogenic Eimeria in dairy cattle herds of Thessaly, Greece, and underscore the importance of integrating rigorous hygiene protocols with age-targeted management to control bovine coccidiosis. Full article

(This article belongs to the Section Molecular Biology)

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27 pages, 7503 KB

Open AccessReview

The Role of the TG2-GPR56 Complex in Cutaneous Squamous Cell Carcinoma (CSCC) Aggression and Therapeutic Resistance

by David J. Weber, Mary E. Cook, Wenbo Yu, Maximino Redondo and Raquel Godoy-Ruiz

Int. J. Mol. Sci. 2026, 27(6), 2902; https://doi.org/10.3390/ijms27062902 - 23 Mar 2026

Viewed by 641

Abstract

Cutaneous squamous cell carcinoma (cSCC) is the second most prevalent skin cancer diagnosed worldwide after basal cell carcinoma. CSCC represents a growing global public health challenge due to its higher potential of local invasion, recurrence, and metastasis. Incidence rates of cSCC are projected [...] Read more.

Cutaneous squamous cell carcinoma (cSCC) is the second most prevalent skin cancer diagnosed worldwide after basal cell carcinoma. CSCC represents a growing global public health challenge due to its higher potential of local invasion, recurrence, and metastasis. Incidence rates of cSCC are projected to increase due to rising exposures to risks factors. Ultraviolet light exposure is the primary cause, and lighter skin pigmentation, immunosuppressive conditions and skin phototype are the primary risk factors. CSCC typically presents as a red, scaly, flat lesion (in situ tumors) or a red, firm, raised lesion with scale or erosion (invasive tumors). Surgical excision remains the standard-of-care for localized cSCC and is often curative. Although, most patients achieve favorable outcomes, a subset of cSCC exhibits a highly aggressive and metastatic phenotype (postoperative recurrence rates are approximately 5%). Addressing the clinical challenge posed by these high-risk cases requires a more comprehensive understanding of the underlying molecular drivers. This review examines the interaction between transglutaminase 2 (TG2) and the G-protein-coupled receptor 56 (GPR56) as a pivotal driver of the aggressive cSCC phenotype. This molecular axis is particularly significant for its role in the maintenance of epidermal cancer stem (ECS) cells, which contribute to tumor progression and therapy resistance. While the definitive link between the TG2-GPR56 complex and systemic metastasis in cSCC is currently being elucidated, significant evidence from analogous malignancies and in vitro keratinocyte models provides a clear mechanistic roadmap for its involvement in tumor invasion. Full article

(This article belongs to the Collection 30th Anniversary of IJMS: Updates and Advances in Biochemistry)

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12 pages, 1268 KB

Open AccessArticle

Impaired T Follicular Regulatory Cell Function and Enhanced T Follicular Helper Cell Activity in Experimental Autoimmune Encephalomyelitis: Mechanistic Insights into CNS Autoimmunity

by Gulam Hekimoglu, Kubra Sevgin, Nurullah Yucel, Gamze Yesilay, Salime Pelin Erguven and Muzaffer Seker

Int. J. Mol. Sci. 2026, 27(6), 2901; https://doi.org/10.3390/ijms27062901 - 23 Mar 2026

Viewed by 1026

Abstract

Multiple sclerosis is a chronic immune-mediated central nervous system disorder marked by neuroinflammation, demyelination, and neurodegeneration, and effectively modeled by experimental autoimmune encephalomyelitis. The objective of this study was to elucidate the roles of T follicular helper and T follicular regulatory cells in [...] Read more.

Multiple sclerosis is a chronic immune-mediated central nervous system disorder marked by neuroinflammation, demyelination, and neurodegeneration, and effectively modeled by experimental autoimmune encephalomyelitis. The objective of this study was to elucidate the roles of T follicular helper and T follicular regulatory cells in the progression of experimental autoimmune encephalomyelitis and to assess their association with IL-21 expression and central nervous system tissue pathology. In this study, experimental autoimmune encephalomyelitis was induced in 25 adult female C57BL/6 mice. Fluorescent double immunostaining for CXCR5 in combination with PD-1, ICOS, CD4, and FOXP3 was performed, along with the analysis of IL-21 mRNA expression. Histopathological assessment was conducted on the cerebrum, cerebellum, and medulla spinalis to evaluate neuroinflammation and myelin loss. A significant increase in CXCR5⁺PD-1⁺ and CXCR5⁺ICOS⁺ T follicular helper-like cells was observed in brain tissue, indicating immune activation and T follicular helper cell involvement. Simultaneously, a marked decrease in FOXP3⁺ T follicular regulatory-like cells suggested impaired immune tolerance and enhanced autoimmune activity. The infiltration of T follicular helper-like cells was identified as a key driver of inflammation and demyelination in the central nervous system. Additionally, the elevated IL-21 mRNA expression highlighted B cell activation and the initiation of antibody-mediated responses. These findings suggest that dysregulation of the T follicular helper/T follicular regulatory axis and elevated IL-21 expression contribute to the immunopathogenesis of experimental autoimmune encephalomyelitis, providing further insight into the mechanisms underlying multiple sclerosis development. Full article

(This article belongs to the Section Molecular Immunology)

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26 pages, 2618 KB

Open AccessArticle

Locus- and Gene-Level Insights into the Inverse Association Between Alzheimer’s Disease and Cancer

by Dipti Debnath, Mohammad Housini, Sanjeev Sariya, Nicole R. Phillips, Gita A. Pathak and Robert C. Barber

Int. J. Mol. Sci. 2026, 27(6), 2900; https://doi.org/10.3390/ijms27062900 - 23 Mar 2026

Viewed by 788

Abstract

Alzheimer’s disease (AD) and cancer are both age-related conditions, yet numerous large-scale epidemiological studies have consistently documented an inverse association, with individuals diagnosed with cancer exhibiting a reduced risk of AD and vice versa. Although this relationship has been replicated across diverse populations, [...] Read more.

Alzheimer’s disease (AD) and cancer are both age-related conditions, yet numerous large-scale epidemiological studies have consistently documented an inverse association, with individuals diagnosed with cancer exhibiting a reduced risk of AD and vice versa. Although this relationship has been replicated across diverse populations, its biological basis remains poorly understood. To address this gap, the present study applies a framework that integrates locus-level genetic correlation (rg) with genetically regulated gene expression to clarify the molecular factors contributing to the inverse epidemiological patterns observed between the two diseases. We used the largest available genome-wide association studies (GWAS) (Nmax = 448,150) to quantify local genetic correlations between AD and several age-associated cancers, including breast, prostate, lung, colorectal, melanoma, basal cell carcinoma, bladder, and endometrial cancer. Eight genomic regions showed significant negative local rg, at the 19q13.31–19q13.32 locus demonstrating strong negative correlations across multiple cancers, including breast, prostate, lung, melanoma, and endometrial cancer. To evaluate the contribution of genetically regulated gene expression, we conducted transcriptome-wide association studies (TWAS) using precomputed gene expression weights from cancer tissues (The Cancer Genome Atlas-TCGA), disease-agnostic tissues (Genotype-Tissue Expression-GTEx), and brain tissue (dorsolateral prefrontal cortex-DLPFC). For each AD–cancer pair, we prioritized genes that were nominally significant in both traits (p < 0.05) and exhibited inverse TWAS Z scores. This analysis identified 24 genes with opposite effect directions between AD and at least three cancer types. TWAS signals also aligned with local rg findings at the 19q13.31–19q13.32 region, suggesting that regulatory variation near this locus contributes to shared but opposing genetic effects beyond the canonical APOE signal. Across cancer types, genes inversely associated with AD converged on pathways involved in cell cycle regulation, apoptosis, DNA-damage response, and metabolic processes. These results support the hypothesis that biological mechanisms promoting proliferation and survival in cancer may oppose those contributing to neurodegeneration in AD. Full article

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

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25 pages, 1904 KB

Open AccessReview

Cannabidiol in Developmental Epilepsy: Organoid-Guided Precision Medicine Across Critical Neurodevelopmental Windows

by Jin Joo, Woo Sub Yang and Hyun Jung Koh

Int. J. Mol. Sci. 2026, 27(6), 2899; https://doi.org/10.3390/ijms27062899 - 23 Mar 2026

Viewed by 757

Abstract

Epilepsy is a progressive network disorder in which recurrent seizures drive maladaptive neurodevelopmental remodeling, cognitive decline, and pharmacoresistance, particularly in developmental epileptic encephalopathies. Cannabidiol (CBD) has emerged as an evidence-based adjunctive therapy for selected childhood-onset epilepsies; however, its broader clinical utility remains limited [...] Read more.

Epilepsy is a progressive network disorder in which recurrent seizures drive maladaptive neurodevelopmental remodeling, cognitive decline, and pharmacoresistance, particularly in developmental epileptic encephalopathies. Cannabidiol (CBD) has emerged as an evidence-based adjunctive therapy for selected childhood-onset epilepsies; however, its broader clinical utility remains limited by heterogeneous responsiveness, restricted indications, and an incomplete understanding of developmental stage–specific efficacy and safety. Here, we synthesize molecular, preclinical and clinical evidence supporting the pleiotropic antiseizure and neuroprotective actions of CBD, including modulation of endocannabinoid-related G protein–coupled receptors, adenosine signaling, transient receptor potential channels, GABAergic maturation, and neuroinflammatory cascades. We highlight critical neurodevelopmental windows during which timely CBD intervention may exert disease-modifying effects by preventing pathological consolidation of hyperexcitable networks. Furthermore, we position human brain organoids as transformative translational platforms that recapitulate early human cortical development and epileptic network dynamics, enabling functional stratification of CBD-responsive phenotypes, developmental safety profiling, and precision therapeutic discovery within human-relevant neural circuits. Collectively, organoid-guided frameworks provide a mechanistic foundation for personalized, developmentally informed CBD therapy and advance precision medicine strategies aimed at modifying epileptogenic trajectories rather than solely suppressing seizures. Full article

(This article belongs to the Topic Applications of Biomedical Technology and Molecular Biological Approach in Brain Diseases, 2nd Edition)

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8 pages, 543 KB

Open AccessCase Report

Upadacitinib-Induced Remission in Multicentric Reticulohistiocytosis: Expanding the Therapeutic Role of JAK Inhibition

by Cristina Pamfil, Mohamed Amin Taki, Elisabeta Candrea, Laura Damian, Maia Ioana Mihon, Diana Maria Margareta Moldovan and Simona Rednic

Int. J. Mol. Sci. 2026, 27(6), 2898; https://doi.org/10.3390/ijms27062898 - 23 Mar 2026

Cited by 1 | Viewed by 481

Abstract

Multicentric reticulohistiocytosis (MRH) is a rare systemic histiocytic disorder of uncertain etiology characterized by papulonodular cutaneous lesions and potentially destructive polyarthritis, with variable multisystem involvement. Owing to its low prevalence, evidence for optimal management remains limited, and treatment responses are heterogeneous. Emerging reports [...] Read more.

Multicentric reticulohistiocytosis (MRH) is a rare systemic histiocytic disorder of uncertain etiology characterized by papulonodular cutaneous lesions and potentially destructive polyarthritis, with variable multisystem involvement. Owing to its low prevalence, evidence for optimal management remains limited, and treatment responses are heterogeneous. Emerging reports suggest that Janus kinase (JAK) inhibition may provide benefit in refractory disease. We report a 60-year-old woman with MRH presenting with papulonodular skin lesions, symmetric polyarthritis, constitutional symptoms, and interstitial lung disease (nonspecific interstitial pneumonia pattern) in the context of co-existing primary biliary cholangitis and no evidence of malignancy. Prior therapies (glucocorticoids, methotrexate, leflunomide) achieved suboptimal control. Upadacitinib, a selective JAK1 inhibitor, induced rapid and complete remission of cutaneous and articular disease with improvement of pulmonary involvement. Secondary weight gain and incident diabetes were managed with tirzepatide. This case adds to the limited literature supporting JAK inhibition as a targeted option for refractory MRH, including multisystem disease with pulmonary involvement. Systematic evaluation of efficacy, durability, and safety is warranted. Full article

(This article belongs to the Special Issue Molecular Basis and Treatment of Skin Diseases and Their Associated Complications (2nd Edition))

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25 pages, 4458 KB

Open AccessReview

Molecular Insights into the Action Mechanism, Resistance Development, and Ecological Risks of Cyantraniliprole

by Jiabao Wu, Xiaohui Liu, Yuqing Peng, Jiguang Huang and Lijuan Zhou

Int. J. Mol. Sci. 2026, 27(6), 2897; https://doi.org/10.3390/ijms27062897 - 23 Mar 2026

Viewed by 713

Abstract

Cyantraniliprole, a second-generation diamide insecticide, exhibits broad-spectrum efficacy against numerous insect pests due to its selective activation of insect ryanodine receptors (RyRs). This activation triggers uncontrolled calcium release from the sarcoplasmic reticulum, resulting in sustained muscle contraction, paralysis, and ultimately death. Its unique [...] Read more.

Cyantraniliprole, a second-generation diamide insecticide, exhibits broad-spectrum efficacy against numerous insect pests due to its selective activation of insect ryanodine receptors (RyRs). This activation triggers uncontrolled calcium release from the sarcoplasmic reticulum, resulting in sustained muscle contraction, paralysis, and ultimately death. Its unique mode of action, which is different from that of organophosphates, carbamates, pyrethroids, and neonicotinoids, helps minimize cross-resistance, making it a valuable component of integrated pest management (IPM). However, continuous field use has led to the development of resistance, primarily mediated by target-site mutations within the RyR transmembrane domain (e.g., G4946E, I4743M, and I4790K) and by enhanced metabolic detoxification via cytochrome P450 monooxygenases, carboxylesterases, and glutathione S-transferases. These mechanisms often confer cross-resistance to other diamide insecticides, thereby complicating resistance management. Moreover, sublethal exposures can disrupt insect growth, development, and reproduction, potentially accelerating resistance evolution. In addition, cyantraniliprole poses ecological risks due to its toxicity to non-target organisms such as aquatic species, including zebrafish and water fleas, pollinators such as honeybees, and soil fauna, as well as the environmental persistence of its major metabolite, J9Z38. This review comprehensively integrated current knowledge on the molecular mechanisms of action, genetic and metabolic bases of resistance, sublethal effects, and ecotoxicological impacts of cyantraniliprole, along with its environmental fate, plant uptake and translocation, and residue dynamics in agricultural systems. Finally, we discuss potential risk-mitigation strategies, including formulation optimization, application-method improvements, and resistance monitoring. Overall, this review aims to provide a comprehensive scientific foundation for the sustainable use, resistance management, and regulatory assessment of this widely used insecticide. Full article

(This article belongs to the Special Issue Innovations in Analytical Chemistry for Environmental and Food Safety: Methodologies and Molecular Insights)

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26 pages, 12977 KB

Open AccessArticle

Assessing the Performance of BioEmu in Understanding Protein Dynamics

by Jinyin Zha, Nuan Li, Mingyu Li, Xinyi Liu, Ruidi Zhu, Li Feng, Xuefeng Lu and Jian Zhang

Int. J. Mol. Sci. 2026, 27(6), 2896; https://doi.org/10.3390/ijms27062896 - 23 Mar 2026

Viewed by 892

Abstract

Understanding the dynamic conformations of proteins is important for rational drug discovery. While molecular dynamics (MD) simulation is the primary tool for this purpose, it is both resource- and time-consuming. Recent advances in deep learning offer an attractive alternative by generating conformational ensembles [...] Read more.

Understanding the dynamic conformations of proteins is important for rational drug discovery. While molecular dynamics (MD) simulation is the primary tool for this purpose, it is both resource- and time-consuming. Recent advances in deep learning offer an attractive alternative by generating conformational ensembles directly from protein sequences. However, the scope of applying such models to protein dynamics studies remains underexplored. Here, we tested the performance of a representative model, BioEmu, across several tasks related to protein dynamics. Our results show that BioEmu can not only generate multiple conformations but also effectively reproduce fundamental properties including residue flexibility, motion correlations, and local residue contacts. However, it fails to predict a mutation-induced shift in conformational distribution and exhibits a preference for higher-energy conformations over lower-energy ones in some cases, indicating that it does not reproduce a right Boltzmann-weighted ensemble. Furthermore, the BioEmu-generated conformations provide only limited improvement in ensemble docking. These findings delineate the current capabilities and limitations of sequence-based generative models for conformational sampling. Also, they highlight several directions for future development—that further energy-based fine-tuning is needed for tasks related to conformational distributions and atom-level generative model is required to study the intermolecular relationship. Full article

(This article belongs to the Section Molecular Informatics)

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20 pages, 3217 KB

Open AccessReview

Investigating the Inflammatory Link Between Vitamin D and Hidradenitis Suppurativa: A Systematic Review and Causal Inference Analysis

by Jasmine Spiteri, Laura Grech, Dillon Mintoff and Nikolai P. Pace

Int. J. Mol. Sci. 2026, 27(6), 2895; https://doi.org/10.3390/ijms27062895 - 23 Mar 2026

Viewed by 825

Abstract

An inverse correlation between serum vitamin D levels and hidradenitis suppurativa (HS) severity is frequently reported, yet the causal nature and direction of this association remain unresolved. A systematic review was conducted following PRISMA guidelines, identifying 12 relevant studies. A two-sample Mendelian randomization [...] Read more.

An inverse correlation between serum vitamin D levels and hidradenitis suppurativa (HS) severity is frequently reported, yet the causal nature and direction of this association remain unresolved. A systematic review was conducted following PRISMA guidelines, identifying 12 relevant studies. A two-sample Mendelian randomization (MR) analysis using the inverse-variance weighted (IVW) method was subsequently performed using genetic instruments for vitamin D from the UK Biobank (n = 417,580) and HS summary statistics from FinnGen (n = 1420). The systematic review confirmed a high prevalence of vitamin D deficiency (<20 ng mL⁻¹) among HS patients (weighted mean 17.90 ng mL⁻¹) and identified inverse correlations between vitamin D levels and disease severity, active lesions, and C-reactive protein (CRP), while supplementation improved clinical outcomes. A null MR estimate consistent with the absence of a detectable average linear causal effect of lifelong genetically predicted 25(OH)D levels on HS risk in the analyzed population was observed. Sensitivity analyses yielded consistent null results with no significant horizontal pleiotropy. The results suggest that hypovitaminosis D is likely a marker of the systemic inflammatory state rather than a direct causative factor. The observed clinical benefits of vitamin D supplementation warrant further interventional studies to define its potential therapeutic role. Full article

(This article belongs to the Special Issue Advances in Genetic and Epigenetic Research in Skin Diseases)

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22 pages, 4922 KB

Open AccessArticle

Spermidine and Eugenol Modulate Tight Junction and Stemness Markers in Colorectal Cancer Spheroids

by Silvia Dilloo, Silvana Hrelia, Cristina Angeloni, Marco Malaguti, Giovanni Dinelli and Francesca Truzzi

Int. J. Mol. Sci. 2026, 27(6), 2894; https://doi.org/10.3390/ijms27062894 - 23 Mar 2026

Viewed by 517

Abstract

Alterations in tight junction (TJ) organization and dysregulation of cancer stem cell (CSC)-associated markers are increasingly recognized as molecular features linked to colorectal cancer (CRC) progression, heterogeneity and clinical outcome. Bioactive dietary compounds such as spermidine (SPD) and eugenol (EUG) have been proposed [...] Read more.

Alterations in tight junction (TJ) organization and dysregulation of cancer stem cell (CSC)-associated markers are increasingly recognized as molecular features linked to colorectal cancer (CRC) progression, heterogeneity and clinical outcome. Bioactive dietary compounds such as spermidine (SPD) and eugenol (EUG) have been proposed as modulators of cancer-related molecular pathways; however, their combined effects on CRC spheroid models relevant to molecular characterization remain insufficiently defined. In the present study, the molecular impact of SPD and EUG, administered individually or in combination, was evaluated in primary and metastatic CRC spheroids. First-generation spheroids derived from Caco-2 and SW620 cells were exposed to SPD, EUG, or SPD+EUG at the time of seeding, and spheroid growth and self-renewal capacity were monitored across successive generations. The expression of TJ- and CSC-associated markers was assessed at both the transcript and protein levels using reverse transcription–quantitative polymerase chain reaction (RT-qPCR), Western blotting and immunohistochemistry. The combined SPD+EUG treatment was associated with a marked reduction in spheroid area and self-renewal capacity in both CRC models. Baseline molecular profiling revealed higher TJ marker expression in Caco-2 spheroids and enrichment of CSC-associated markers in SW620 spheroids. Treatment-induced modulation of CSC- and TJ-related transcripts was observed; however, transcript-level changes were not consistently mirrored at the protein level, indicating the involvement of post-transcriptional regulatory mechanisms. In particular, Occludin (OCLN), Zonula occludens-1 (ZO-1), CD133, ALDH1A1, SOX2 and VE-cadherin exhibited divergent RNA and protein expression patterns depending on cell type and treatment condition. Collectively, these findings underscore the relevance of three-dimensional CRC spheroid models for molecular profiling studies and highlight the importance of integrating transcript- and protein-level analyses when evaluating bioactive compounds with potential diagnostic and translational relevance in colorectal cancer. Full article

(This article belongs to the Special Issue Molecular Diagnosis and Treatment of Colorectal Cancer)

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17 pages, 2472 KB

Open AccessArticle

The La Region of Foot-and-Mouth Disease Virus: Essential for L Protein Cellular Distribution but Not Functional Activity

by Mengting Cai, Hong Yuan, Tao Wang, Yuanfang Fu, Huifang Bao, Pinghua Li, Han Weng, Junfang Zhao, Kun Li, Pu Sun, Xueqing Ma, Zhixun Zhao, Jing Zhang, Yimei Cao, Dong Li, Zengjun Lu and Xingwen Bai

Int. J. Mol. Sci. 2026, 27(6), 2893; https://doi.org/10.3390/ijms27062893 - 23 Mar 2026

Viewed by 432

Abstract

Foot-and-mouth disease virus (FMDV) is a highly contagious picornavirus that affects cloven-hoofed animals and carries significant economic implications for the global livestock industry. FMDV features two Leader (L) protein isoforms, Lab and Lb, differing at their amino termini by 28 amino acids (La [...] Read more.

Foot-and-mouth disease virus (FMDV) is a highly contagious picornavirus that affects cloven-hoofed animals and carries significant economic implications for the global livestock industry. FMDV features two Leader (L) protein isoforms, Lab and Lb, differing at their amino termini by 28 amino acids (La region). Currently, the activity of La protein sequences has not been investigated. To address this issue, the comparison study of biological and functional roles of Lab and Lb was performed as the La region alone did not independently perform protein function. We found that Lab and Lb significantly regulated FMDV replication and pathogenicity, and their coexistence afforded optimal FMDV properties. Subsequently, we observed that both L isoforms cleaved eukaryotic translation initiation factor 4G (eIF4G) I, suppressed type I and type III interferon (IFN) expression, and exhibited marked cytotoxicity, indicating that they were all key components in FMDV’s antagonism of host antiviral defenses. Finally, the subcellular distribution of Lab and Lb was detected. Despite dual localization in cytoplasmic and nuclear compartments, both isoforms displayed different spatial distribution patterns, and Lb induced more pronounced morphological changes to host cells than Lab. Furthermore, bioinformatics predicted that the La region might contain a non-classical secretory signal peptide, potentially facilitating Lab distribution to the cell membrane or extracellular space. Collectively, the primary encoding role of La region was to control the intracellular distribution of L protein, as opposed to regulating its functional activity. This study may help to deepen our understanding of why FMDV encoded two isoforms of L protein. Full article

(This article belongs to the Special Issue Molecular and Cell Biology of Viruses)

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20 pages, 2056 KB

Open AccessArticle

Direct Production of 2-Butanol from Glucose by Recombinant Klebsiella pneumoniae Strains

by Emanoel Gergov, Alexander Arsov, Kaloyan Petrov, Lidia Tsigoriyna and Penka Petrova

Int. J. Mol. Sci. 2026, 27(6), 2892; https://doi.org/10.3390/ijms27062892 - 23 Mar 2026

Viewed by 423

Abstract

2-Butanol is a promising biofuel due to its favorable properties and lower microbial toxicity compared to other butanol isomers. However, microbial production remains challenging due to the absence of a native biochemical pathway for directly converting sugars into 2-butanol. To achieve this goal, [...] Read more.

2-Butanol is a promising biofuel due to its favorable properties and lower microbial toxicity compared to other butanol isomers. However, microbial production remains challenging due to the absence of a native biochemical pathway for directly converting sugars into 2-butanol. To achieve this goal, glucose should be directed through the 2,3-butanediol (2,3-BD) pathway, involving α-acetolactate synthase, α-acetolactate decarboxylase, and butanediol dehydrogenase for the formation of meso-2,3-BD, followed by diol dehydratase-catalyzed conversion of meso-2,3-BD to butanone and alcohol dehydrogenase-mediated reduction in butanone to 2-butanol. In this study, we report the development of six new recombinant strains based on Klebsiella pneumoniae G31, in which the metabolic pathway for converting glucose to meso-2,3-BD was extended to 2-butanol. All engineered strains harbored the vitamin B₁₂-dependent diol dehydratase complex (pduCDEGH) from Lentilactobacillus diolivorans DSM 14421 under its native promoter control. In addition, pduQ from the same strain, and adh from Clostridium beijerinckii DSM 51 encoding alcohol dehydrogenases were expressed under native, T7, or Ptac promoters. The highest yield of 2-butanol from glucose was achieved by K. pneumoniae K6 carrying the adh gene under the control of the T7 promoter—437 mg/L. Using 2-butanone as a substrate, K6 again produced the highest titer of 2-butanol (3.9 g/L), followed by the recombinant K8 (with adh under the Ptac promoter), and notably, by the native K. pneumoniae strains. Therefore, although pduQ encodes a key alcohol dehydrogenase in L. diolivorans, it has weaker properties than adh for the K. pneumoniae host in all promoter configurations. As the high expression levels of adh under T7 promoter control were driven by the native bacterial RNA polymerase, this promoter–host combination appears particularly suitable for developing other strains of industrial relevance. Full article

(This article belongs to the Special Issue Molecular Research on Bacteria: 2nd Edition)

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24 pages, 2149 KB

Open AccessReview

Tracheal Regeneration: Recent Progress in the Application of Stem Cells in Tracheal Bioengineering

by Fatemeh Ganji, Florian Le Billan, Siba Haykal and Golnaz Karoubi

Int. J. Mol. Sci. 2026, 27(6), 2891; https://doi.org/10.3390/ijms27062891 - 23 Mar 2026

Viewed by 636

Abstract

Traumatic injury, stenosis, and malignancy involving large segments of the airway are difficult to reconstruct and require novel solutions. Despite advances in surgical techniques, the reconstruction of long-segment tracheal defects remains a significant challenge. Several bioengineering approaches have been explored for tracheal regeneration [...] Read more.

Traumatic injury, stenosis, and malignancy involving large segments of the airway are difficult to reconstruct and require novel solutions. Despite advances in surgical techniques, the reconstruction of long-segment tracheal defects remains a significant challenge. Several bioengineering approaches have been explored for tracheal regeneration in vitro and in vivo, using cells in combination with three dimentional (3D) biological or synthetic scaffolds. This paper reviews recent advances in developing bioengineered trachea and the technologies utilized toward generating transplantable tracheal grafts. Specifically, the review will focus on the recellularization of tissue-engineered grafts using natural or synthetic scaffolds, highlighting relevant cell types used to reconstitute tracheal epithelium and cartilage. The promise of newly explored paradigms, including the application of pluripotent stem cells, will be discussed with an overview of associated challenges and necessary steps for future translation. Overall, these advances provide a foundation for the development of clinically viable tracheal grafts, bringing engineered tracheal reconstruction closer to reality. Full article

(This article belongs to the Special Issue Regenerative Medicine: Biomaterials and Stem Cell Research: 2nd Edition)

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14 pages, 2413 KB

Open AccessReview

Mitochondrial DNA Modification in Assisted Reproduction: Concept to Practice—A Narrative Review

by Mariam Mehwish Mohsin, Misbah Azher, Fatima Asghar, Hiba Habeebu Rahiman, Rajani Dube, Subhranshu Sekhar Kar, Shadha Nasser Mohammed Bahutair, Bellary Kuruba Manjunatha Goud and Swayam Siddha Kar

Int. J. Mol. Sci. 2026, 27(6), 2890; https://doi.org/10.3390/ijms27062890 - 23 Mar 2026

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Abstract

Mitochondria play a fundamental role in human reproduction by supplying the energy required for key early reproductive processes. As mitochondrial Deoxyribonucleic acid (mtDNA) is maternally inherited, pathogenic mutations can lead to multisystem disorders that are transmitted to offspring. Mitochondrial replacement therapy (MRT) has [...] Read more.

Mitochondria play a fundamental role in human reproduction by supplying the energy required for key early reproductive processes. As mitochondrial Deoxyribonucleic acid (mtDNA) is maternally inherited, pathogenic mutations can lead to multisystem disorders that are transmitted to offspring. Mitochondrial replacement therapy (MRT) has emerged as a promising assisted reproductive approach to prevent the transmission of pathogenic mtDNA by replacing defective mitochondria with healthy donor mitochondria. There have been recent reports of successful MRT in humans. However, MRT remains a relatively new procedure and needs further experiments to establish its long-term safety and effectiveness. Overall, mitochondrial replacement therapy holds significant promise in helping families build healthier futures. This review explores the evolution of mitochondrial DNA modification in reproductive cells and addresses the associated ethical considerations, including acceptable clinical indications, reproductive choices, and long-term considerations for affected children. Full article

(This article belongs to the Special Issue Molecular Research on Reproductive Physiology and Endocrinology)

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Int. J. Mol. Sci., Volume 27, Issue 6 (March-2 2026) – 402 articles

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