International Journal of Molecular Sciences

12 pages, 1135 KiB

Open AccessArticle

Exploring Adverse Event Associations of Predicted PXR Agonists Using the FAERS Database

by Saki Yamada and Yoshihiro Uesawa

Int. J. Mol. Sci. 2025, 26(15), 7630; https://doi.org/10.3390/ijms26157630 (registering DOI) - 6 Aug 2025

Pregnane X receptor (PXR) is an important nuclear receptor that regulates diverse physiological functions, including drug metabolism. Although PXR activation is potentially involved in adverse events, the full scope of its impact has yet to be elucidated. In this study, we developed a [...] Read more.

Pregnane X receptor (PXR) is an important nuclear receptor that regulates diverse physiological functions, including drug metabolism. Although PXR activation is potentially involved in adverse events, the full scope of its impact has yet to be elucidated. In this study, we developed a machine learning model to predict the activity of PXR agonists and applied the model to drugs listed in the US Food and Drug Administration Adverse Event Reporting System database. Analysis of the predicted agonist–active drug interactions and adverse event reports revealed statistically significant risks (lnROR > 1 and −logp > 1.3) for multiple cardiac disorders. These findings suggest that PXR activity is involved in cardiovascular adverse effects and may contribute to drug safety through the early identification of risks. Full article

(This article belongs to the Special Issue In Silico Approaches to Unravelling Toxicity Mechanisms in Molecular Drugs)

34 pages, 1221 KiB

Open AccessReview

Unmasking Pediatric Asthma: Epigenetic Fingerprints and Markers of Respiratory Infections

by Alessandra Pandolfo, Rosalia Paola Gagliardo, Valentina Lazzara, Andrea Perri, Velia Malizia, Giuliana Ferrante, Amelia Licari, Stefania La Grutta and Giusy Daniela Albano

Int. J. Mol. Sci. 2025, 26(15), 7629; https://doi.org/10.3390/ijms26157629 - 6 Aug 2025

Abstract

Pediatric asthma is a multifactorial and heterogeneous disease determined by the dynamic interplay of genetic susceptibility, environmental exposures, and immune dysregulation. Recent advances have highlighted the pivotal role of epigenetic mechanisms, in particular, DNA methylation, histone modifications, and non-coding RNAs, in the regulation [...] Read more.

Pediatric asthma is a multifactorial and heterogeneous disease determined by the dynamic interplay of genetic susceptibility, environmental exposures, and immune dysregulation. Recent advances have highlighted the pivotal role of epigenetic mechanisms, in particular, DNA methylation, histone modifications, and non-coding RNAs, in the regulation of inflammatory pathways contributing to asthma phenotypes and endotypes. This review examines the role of respiratory viruses such as respiratory syncytial virus (RSV), rhinovirus (RV), and other bacterial and fungal infections that are mediators of infection-induced epithelial inflammation that drive epithelial homeostatic imbalance and induce persistent epigenetic alterations. These alterations lead to immune dysregulation, remodeling of the airways, and resistance to corticosteroids. A focused analysis of T2-high and T2-low asthma endotypes highlights unique epigenetic landscapes directing cytokines and cellular recruitment and thereby supports phenotype-specific aspects of disease pathogenesis. Additionally, this review also considers the role of miRNAs in the control of post-transcriptional networks that are pivotal in asthma exacerbation and the severity of the disease. We discuss novel and emerging epigenetic therapies, such as DNA methyltransferase inhibitors, histone deacetylase inhibitors, miRNA-based treatments, and immunomodulatory probiotics, that are in preclinical or early clinical development and may support precision medicine in asthma. Collectively, the current findings highlight the translational relevance of including pathogen-related biomarkers and epigenomic data for stratifying pediatric asthma patients and for the personalization of therapeutic regimens. Epigenetic dysregulation has emerged as a novel and potentially transformative approach for mitigating chronic inflammation and long-term morbidity in children with asthma. Full article

(This article belongs to the Special Issue Molecular Research in Airway Diseases)

10 pages, 477 KiB

Open AccessArticle

Immunogenetics of Multiple Sclerosis in Romanian Patients: Preliminary Data

by Alexandra Elena Constantinescu, Ion Mărunțelu, Andreea Pleșa, Carmen Adella Sîrbu, Florentina Cristina Pleșa, Andreia Ioana Constantinescu and Ileana Constantinescu

Int. J. Mol. Sci. 2025, 26(15), 7628; https://doi.org/10.3390/ijms26157628 - 6 Aug 2025

Abstract

Multiple sclerosis (MS) is a chronic autoimmune disease characterized by the immune system attacking the central nervous system, leading to demyelination and neurodegeneration. This work investigates the relationship between specific human leukocyte antigen (HLA) polymorphisms and MS, aiming to reveal the immunogenetic background [...] Read more.

Multiple sclerosis (MS) is a chronic autoimmune disease characterized by the immune system attacking the central nervous system, leading to demyelination and neurodegeneration. This work investigates the relationship between specific human leukocyte antigen (HLA) polymorphisms and MS, aiming to reveal the immunogenetic background of this disease for more individualized management approaches. This study employed a case–control design, analyzing HLA allele frequencies in 179 MS patients and 200 control subjects using next-generation sequencing, The key findings indicate significant associations between several HLA Class I and II alleles and MS, including HLA-B*35:03:01:03, HLA-C*04:01:01:14, HLA-DRB1*15:01:01:26, and HLA-DQA1*05:05:01:02. These findings emphasize the critical role of HLA molecules in MS Romanian patients. Full article

(This article belongs to the Section Molecular Immunology)

13 pages, 917 KiB

Open AccessArticle

Relationship Between Prostaglandin and Interleukin Concentrations in Seminal Fluid and Their Influence on the Rate of Fertilization in Men Undergoing ICSI

by Houda Amor, Fatina W. Dahadhah, Peter Michael Jankowski, Rami Al Nasser, Lisa Jung, Ingolf Juhasz-Böss, Erich Franz Solomayer and Mohamad Eid Hammadeh

Int. J. Mol. Sci. 2025, 26(15), 7627; https://doi.org/10.3390/ijms26157627 (registering DOI) - 6 Aug 2025

Abstract

Sperm count, motility, and morphology are semen parameters that directly affect male fertility. The presence of cytokines in seminal plasma negatively or positively influences these parameters. Interleukins and prostaglandins are proinflammatory cytokines present in human seminal plasma and play crucial roles in fertilization, [...] Read more.

Sperm count, motility, and morphology are semen parameters that directly affect male fertility. The presence of cytokines in seminal plasma negatively or positively influences these parameters. Interleukins and prostaglandins are proinflammatory cytokines present in human seminal plasma and play crucial roles in fertilization, in general and after intracytoplasmic sperm injection (ICSI) procedures. This study aimed to investigate the possible influence of interleukins IL-17 and IL-18, and prostaglandins PGE2 and PGF2α on male infertility. Semen samples were collected from 58 males who underwent the ICSI procedure. An enzyme-linked immunosorbent assay (ELISA) was used to determine the levels of IL-17, IL-18, PGE2, and PGF2α, and these concentrations were then correlated with semen parameters and the rate of fertilization. Furthermore, the chromatin integrity of the sperm was evaluated with an Acridine Orange (AO) assay. The results showed an inversely proportional relationship between the AO binding intensity and fertilization rate (r = −0.394; p ≤ 0.002). Furthermore, a negative correlation was observed between the IL-18 concentration and positive AO (p ≤ 0.021). Moreover, the IL-18 concentration was positively correlated with the fertilization rate (p ≤ 0.05). In contrast, IL-17 did not significantly correlate with any semen parameters or with the fertilization rate. Seminal PGE2 levels were significantly correlated with embryo cleavage at 72 h (p ≤ 0.05). To conclude, this study revealed that denaturation of sperm nuclear deoxyribonucleic acid (DNA) contributes to low fertilization rates. In addition, this study proposed a potential role for IL-18 in fertilization. PGE2 likely influences embryo development, but further studies are needed to examine the impact of seminal PGE2 on the oocyte to fully elucidate its contribution to this complex biological process. Full article

(This article belongs to the Special Issue Advances in Spermatogenesis and Male Infertility)

19 pages, 1349 KiB

Open AccessArticle

A Retrospective Study of Clinical and Genetic Features in a Long-Term Cohort of Mexican Children with Alagille Syndrome

by Rodrigo Vázquez-Frias, Gustavo Varela-Fascinetto, Carlos Patricio Acosta-Rodríguez-Bueno, Alejandra Consuelo, Ariel Carrillo, Magali Reyes-Apodaca, Rodrigo Moreno-Salgado, Jaime López-Valdez, Elizabeth Hernández-Chávez, Beatriz González-Ortiz, José F Cadena-León, Salvador Villalpando-Carrión, Liliana Worona-Dibner, Valentina Martínez-Montoya, Arantza Cerón-Muñiz, Edgar Ramírez-Ramírez and Tania Barragán-Arévalo

Int. J. Mol. Sci. 2025, 26(15), 7626; https://doi.org/10.3390/ijms26157626 - 6 Aug 2025

Abstract

Alagille syndrome (ALGS) is a multisystem disorder characterized by a paucity of intrahepatic bile ducts and cholestasis, often requiring liver transplantation before adulthood. Due to the lack of genotype–phenotype correlation, case series are essential to understand disease presentation and prognosis. Data on Mexican [...] Read more.

Alagille syndrome (ALGS) is a multisystem disorder characterized by a paucity of intrahepatic bile ducts and cholestasis, often requiring liver transplantation before adulthood. Due to the lack of genotype–phenotype correlation, case series are essential to understand disease presentation and prognosis. Data on Mexican ALGS patients are limited. Therefore, we aimed to characterize a large series of Mexican patients by consolidating cases from major institutions and independent geneticists, with the goal of generating one of the most comprehensive cohorts in Latin America. We retrospectively analyzed clinical records of pediatric ALGS patients, focusing on demographics, clinical features, laboratory and imaging results, biopsy findings, and transplant status. Genetic testing was performed for all cases without prior molecular confirmation. We identified 52 ALGS cases over 13 years; 22 had available clinical records. Of these, only 6 had molecular confirmation at study onset, prompting genetic testing in the remaining 16. We identified six novel JAG1 variants and several previously unreported phenotypic features. A liver transplantation rate of 13% was observed in the cohort. This study represents the largest molecularly confirmed ALGS cohort in Mexico to date. Novel genetic and clinical findings expand the known spectrum of ALGS and emphasize the need for improved therapies, such as IBAT inhibitors, which may alleviate symptoms and reduce the need for transplantation. Full article

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

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19 pages, 3275 KiB

Open AccessArticle

Polysialylation of Glioblastoma Cells Is Regulated by Autophagy Under Nutrient Deprivation

by Sofia Scibetta, Giuseppe Pepe, Marco Iuliano, Alessia Iaiza, Elisabetta Palazzo, Marika Quadri, Thomas J. Boltje, Francesco Fazi, Vincenzo Petrozza, Sabrina Di Bartolomeo, Alba Di Pardo, Antonella Calogero, Giorgio Mangino, Vittorio Maglione and Paolo Rosa

Int. J. Mol. Sci. 2025, 26(15), 7625; https://doi.org/10.3390/ijms26157625 - 6 Aug 2025

Abstract

Glioblastoma (GBM) is a highly aggressive brain tumor marked by invasive growth and therapy resistance. Tumor cells adapt to hostile conditions, such as hypoxia and nutrient deprivation, by activating survival mechanisms including autophagy and metabolic reprogramming. Among GBM-associated changes, hypersialylation, particularly, the aberrant [...] Read more.

Glioblastoma (GBM) is a highly aggressive brain tumor marked by invasive growth and therapy resistance. Tumor cells adapt to hostile conditions, such as hypoxia and nutrient deprivation, by activating survival mechanisms including autophagy and metabolic reprogramming. Among GBM-associated changes, hypersialylation, particularly, the aberrant expression of polysialic acid (PSA), has been linked to increased plasticity, motility, and immune evasion. PSA, a long α2,8-linked sialic acid polymer typically attached to the NCAM, is abundant in the embryonic brain and re-expressed in cancers, correlating with poor prognosis. Here, we investigated how PSA expression was regulated in GBM cells under nutrient-limiting conditions. Serum starvation induced a marked increase in PSA-NCAM, driven by upregulation of the polysialyltransferase ST8SiaIV and an autophagy-dependent recycling of sialic acids from degraded glycoproteins. Inhibition of autophagy or sialidases impaired PSA induction, and PSA regulation appeared dependent on p53 function. Immunohistochemical analysis of GBM tissues revealed co-localization of PSA and LC3, particularly around necrotic regions. In conclusion, we identified a novel mechanism by which GBM cells sustain PSA-NCAM expression via autophagy-mediated sialic acid recycling under nutrient stress. This pathway may enhance cell migration, immune escape, and stem-like properties, offering a potential therapeutic target in GBM. Full article

(This article belongs to the Special Issue Targeting Glioblastoma Metabolism)

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21 pages, 3451 KiB

Open AccessArticle

Transcriptional Repression of CCL2 by K_Ca3.1 K⁺ Channel Activation and LRRC8A Anion Channel Inhibition in THP-1-Differentiated M₂ Macrophages

by Miki Matsui, Junko Kajikuri, Hiroaki Kito, Yohei Yamaguchi and Susumu Ohya

Int. J. Mol. Sci. 2025, 26(15), 7624; https://doi.org/10.3390/ijms26157624 - 6 Aug 2025

Abstract

We investigated the role of the intermediate-conductance, Ca²⁺-activated K⁺ channel K_Ca3.1 and volume-regulatory anion channel LRRC8A in regulating C-C motif chemokine ligand 2 (CCL2) expression in THP-1-differentiated M₂ macrophages (M₂-MACs), which serve as a useful [...] Read more.

We investigated the role of the intermediate-conductance, Ca²⁺-activated K⁺ channel K_Ca3.1 and volume-regulatory anion channel LRRC8A in regulating C-C motif chemokine ligand 2 (CCL2) expression in THP-1-differentiated M₂ macrophages (M₂-MACs), which serve as a useful model for studying tumor-associated macrophages (TAMs). CCL2 is a potent chemoattractant involved in the recruitment of immunosuppressive cells and its expression is regulated through intracellular signaling pathways such as ERK, JNK, and Nrf2 in various types of cells including macrophages. The transcriptional expression of CCL2 was suppressed in M₂-MACs following treatment with a K_Ca3.1 activator or an LRRC8A inhibitor via distinct signaling pathways: ERK–CREB2 and JNK–c-Jun pathways for K_Ca3.1, and the NOX2–Nrf2–CEBPB pathway for LRRC8A. Under in vitro conditions mimicking the elevated extracellular K⁺ concentration ([K⁺]_e) characteristic of the tumor microenvironment (TME), CCL2 expression was markedly upregulated, and this increase was reversed by treatment with them in M₂-MACs. Additionally, the WNK1–AMPK pathway was, at least in part, involved in the high [K⁺]_e-induced upregulation of CCL2. Collectively, modulating K_Ca3.1 and LRRC8A activities offers a promising strategy to suppress CCL2 secretion in TAMs, potentially limiting the CCL2-induced infiltration of immunosuppressive cells (TAMs, T_regs, and MDSCs) in the TME. Full article

(This article belongs to the Special Issue Regulation of Ion Channels and Transporters)

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19 pages, 1548 KiB

Open AccessArticle

Phytochemical Analysis, Antioxidant Activity, and Anticancer Potential of Afzelia quanzensis Welw—Bark Extract: A Traditional Remedy Utilized by Indigenous Communities in KwaZulu-Natal and Eastern Cape Provinces of South Africa

by Siphamandla Qhubekani Njabuliso Lamula, Thando Bhanisa, Martha Wium, Juliano Domiraci Paccez, Luiz Fernando Zerbini and Lisa V. Buwa-Komoreng

Int. J. Mol. Sci. 2025, 26(15), 7623; https://doi.org/10.3390/ijms26157623 - 6 Aug 2025

Abstract

Despite the significant advancements in treatment and prevention, the fight against cancer is ongoing worldwide. This study evaluated the pharmacological properties and anticancer activity of Afzelia quanzensis bark, traditionally used by the indigenous communities of KwaZulu Natal and Eastern Cape Provinces of South [...] Read more.

Despite the significant advancements in treatment and prevention, the fight against cancer is ongoing worldwide. This study evaluated the pharmacological properties and anticancer activity of Afzelia quanzensis bark, traditionally used by the indigenous communities of KwaZulu Natal and Eastern Cape Provinces of South Africa to treat cancer and related illnesses. Phytochemical screening, high-performance liquid chromatography–diode array detection (HPLC-DAD), and Fourier-transform infrared spectroscopy (FTIR) analyses were carried out using established protocols. The antioxidant activity was assessed via the 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging capacity and nitric oxide radicals. The anticancer activity was evaluated using the MTT assay (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide). Phytochemical analysis revealed the presence of saponins, flavonoids, terpenoids, alkaloids, steroids, cardiac glycosides, and phlobatannins. The HPLC-DAD analysis detected seven distinctive peaks in the aqueous extract and three distinctive peaks in the methanolic extract. The FTIR spectra of the aqueous extract displayed characteristic peaks corresponding to O-H, C=O, C=C, and =C–H functional groups. Among the tested extracts, the methanol extract exhibited the strongest antioxidant activity, followed by the ethanolic extract, in both DPPH and nitric oxide. The methanol extract showed a higher cell proliferation inhibition against the DU-145 cancer cell line with the percentage of inhibition of 37.8%, followed by the aqueous extract with 36.3%. In contrast, limited activity was observed against PC-3, SK-UT-1, and AGS cell lines. The results demonstrated notable dose-dependent antioxidant and antiproliferative activities supporting the ethnomedicinal use of Afzelia quanzensis bark in cancer management. These findings warrant further investigation into its bioactive constituents and mechanisms of action. Full article

(This article belongs to the Section Bioactives and Nutraceuticals)

19 pages, 1680 KiB

Open AccessArticle

Role of Endogenous Galectin-3 on Cell Biology of Immortalized Retinal Pigment Epithelial Cells In Vitro †

by Caspar Liesenhoff, Marlene Hillenmayer, Caroline Havertz, Arie Geerlof, Daniela Hartmann, Siegfried G. Priglinger, Claudia S. Priglinger and Andreas Ohlmann

Int. J. Mol. Sci. 2025, 26(15), 7622; https://doi.org/10.3390/ijms26157622 - 6 Aug 2025

Abstract

Galectin-3 is a multifunctional protein that is associated with diseases of the chorioretinal interface, in which the retinal pigment epithelium (RPE) plays a central role in disease development and progression. Since galectin-3 can function extracellularly as well as intracellularly via different mechanisms, [...] Read more.

Galectin-3 is a multifunctional protein that is associated with diseases of the chorioretinal interface, in which the retinal pigment epithelium (RPE) plays a central role in disease development and progression. Since galectin-3 can function extracellularly as well as intracellularly via different mechanisms, we developed an immortalized human RPE cell line (ARPE-19) with a knockdown for galectin-3 expression (ARPE-19/LGALS3^+/−) using a sgRNA/Cas9 all-in-one expression vector. By Western blot analysis, a reduced galectin-3 expression of approximately 48 to 60% in heterozygous ARPE-19/LGALS3^+/− cells was observed when compared to native controls. Furthermore, ARPE-19/LGALS3^+/− cells displayed a flattened, elongated phenotype with decreased E-cadherin as well as enhanced N-cadherin and α-smooth muscle actin mRNA expression, indicating an epithelial–mesenchymal transition of the cells. Compared to wildtype controls, ARPE-19/LGALS3^+/− cells had significantly reduced metabolic activity to 86% and a substantially decreased proliferation to 73%. Furthermore, an enhanced cell adhesion and a diminished migration of immortalized galectin-3 knockdown RPE cells was observed compared to native ARPE-19 cells. Finally, by Western blot analysis, reduced pAKT, pERK1/2, and β-catenin signaling were detected in ARPE-19/LGALS3^+/− cells when compared to wildtype controls. In summary, in RPE cells, endogenous galectin-3 appears to be essential for maintaining the epithelial phenotype as well as cell biological functions such as metabolism, proliferation, or migration, effects that might be mediated via a decreased activity of the AKT, ERK1/2, and β-catenin signaling pathways. Full article

(This article belongs to the Special Issue Galectins (Gals), 2nd Edition)

15 pages, 3316 KiB

Open AccessArticle

Evaluation of Collagenic Porcine Bone Blended with a Collagen Gel for Bone Regeneration: An In Vitro Study

by Tania Vanessa Pierfelice, Chiara Cinquini, Morena Petrini, Emira D’Amico, Camillo D’Arcangelo, Antonio Barone and Giovanna Iezzi

Int. J. Mol. Sci. 2025, 26(15), 7621; https://doi.org/10.3390/ijms26157621 - 6 Aug 2025

Abstract

A thermosensitive collagen-based gel (TSV gel), containing type I and III collagen, has been developed to improve the handling and stability of bone graft materials. However, its direct effect on osteoblasts is not well understood. This in vitro study evaluated the biological response [...] Read more.

A thermosensitive collagen-based gel (TSV gel), containing type I and III collagen, has been developed to improve the handling and stability of bone graft materials. However, its direct effect on osteoblasts is not well understood. This in vitro study evaluated the biological response of human oral osteoblasts to four bone substitutes: OsteoBiol^® GTO^® (larger granules with 20% TSV gel), Gen-OS^® (smaller granules), Gen-OS^® combined with 50% TSV gel (Gen-OS^®+TSV), and TSV gel alone. Cell proliferation, adhesion, morphology, collagen and calcium deposition, alkaline phosphatase (ALP) activity, gene expression of osteogenic markers and integrins, and changes in pH and extracellular calcium and phosphate levels were investigated. All materials supported osteoblast activity, but Gen-OS+TSV and GTO showed the most pronounced effects. These two groups promoted better cell adhesion and proliferation, higher ALP activity, and greater matrix mineralization. GTO improved cell adhesion, while the addition of TSV gel to Gen-OS enhanced biological responses compared with Gen-OS alone. Integrins α2, α5, β1, and β3, important for cell attachment to collagen, were notably upregulated in Gen-OS+TSV and GTO. Both groups also showed increased expression of osteogenic markers such as BMP-2, ALP, and osteocalcin (OCN). Higher extracellular ion concentrations and a more alkaline pH were observed, particularly in conditions without cells, suggesting active ion uptake by osteoblasts. In conclusion, combining TSV gel with collagen-based granules improves the cellular environment for osteoblast activity and may support bone regeneration more effectively than using either component alone. Full article

(This article belongs to the Special Issue Molecular Studies of Bone Biology and Bone Tissue: 2nd Edition)

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13 pages, 3790 KiB

Open AccessArticle

Anti-CD26 Antibody Suppresses Epithelial-Mesenchymal Transition in Colorectal Cancer Stem Cells

by Takumi Iwasawa, Ryo Hatano, Satoshi Takeda, Ayumi Kurusu, Chikako Okamoto, Kazunori Kato, Chikao Morimoto and Noriaki Iwao

Int. J. Mol. Sci. 2025, 26(15), 7620; https://doi.org/10.3390/ijms26157620 - 6 Aug 2025

Abstract

CD26 (dipeptidyl peptidase-4) is a marker of colorectal cancer stem cells with high metastatic potential and resistance to therapy. Although CD26 expression is known to be associated with tumor progression, its functional involvement in epithelial-mesenchymal transition (EMT) and metastasis remains to be fully [...] Read more.

CD26 (dipeptidyl peptidase-4) is a marker of colorectal cancer stem cells with high metastatic potential and resistance to therapy. Although CD26 expression is known to be associated with tumor progression, its functional involvement in epithelial-mesenchymal transition (EMT) and metastasis remains to be fully elucidated. In this study, we aimed to investigate the effects of a monoclonal anti-CD26 antibody on EMT-related phenotypes and metastatic behavior in colorectal cancer cells. We evaluated changes in EMT markers by quantitative PCR and Western blotting, assessed cell motility and invasion using scratch wound-healing and Transwell assays, and examined metastatic potential in vivo using a splenic injection mouse model. Treatment with the anti-CD26 antibody significantly increased the expression of the epithelial marker E-cadherin and reduced levels of EMT-inducing transcription factors, including ZEB1, Twist1, and Snail1, at the mRNA and protein levels. Functional assays revealed that the antibody markedly inhibited cell migration and invasion in vitro without exerting cytotoxic effects. Furthermore, systemic administration of the anti-CD26 antibody significantly suppressed the formation of liver metastases in vivo. These findings suggest that CD26 may contribute to the regulation of EMT and metastatic behavior in colorectal cancer. Our data highlight the potential therapeutic utility of CD26-targeted antibody therapy for suppressing EMT-associated phenotypes and metastatic progression. Full article

(This article belongs to the Special Issue Molecular Mechanisms and Therapies of Colorectal Cancer: 4th Edition)

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41 pages, 865 KiB

Open AccessReview

Navigating the Landscape of Liquid Biopsy in Colorectal Cancer: Current Insights and Future Directions

by Pina Ziranu, Andrea Pretta, Giorgio Saba, Dario Spanu, Clelia Donisi, Paolo Albino Ferrari, Flaviana Cau, Alessandra Pia D’Agata, Monica Piras, Stefano Mariani, Marco Puzzoni, Valeria Pusceddu, Ferdinando Coghe, Gavino Faa and Mario Scartozzi

Int. J. Mol. Sci. 2025, 26(15), 7619; https://doi.org/10.3390/ijms26157619 - 6 Aug 2025

Abstract

Liquid biopsy has emerged as a valuable tool for the detection and monitoring of colorectal cancer (CRC), providing minimally invasive insights into tumor biology through circulating biomarkers such as circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), microRNAs (miRNAs), long non-coding RNAs (lncRNAs), [...] Read more.

Liquid biopsy has emerged as a valuable tool for the detection and monitoring of colorectal cancer (CRC), providing minimally invasive insights into tumor biology through circulating biomarkers such as circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Additional biomarkers, including tumor-educated platelets (TEPs) and exosomal RNAs, offer further potential for early detection and prognostic role, although ongoing clinical validation is still needed. This review summarizes the current evidence on the diagnostic, prognostic, and predictive capabilities of liquid biopsy in both metastatic and non-metastatic CRC. In the non-metastatic setting, liquid biopsy is gaining traction in early detection through screening and in identifying minimal residual disease (MRD), potentially guiding adjuvant treatment and reducing overtreatment. In contrast, liquid biopsy is more established in metastatic CRC for monitoring treatment responses, clonal evolution, and mechanisms of resistance. The integration of ctDNA-guided treatment algorithms into clinical practice could optimize therapeutic strategies and minimize unnecessary interventions. Despite promising advances, challenges remain in assay standardization, early-stage sensitivity, and the integration of multi-omic data for comprehensive tumor profiling. Future efforts should focus on enhancing the sensitivity of liquid biopsy platforms, validating emerging biomarkers, and expanding multi-omic approaches to support more targeted and personalized treatment strategies across CRC stages. Full article

(This article belongs to the Special Issue Cancer Biology and Epigenetic Modifications)

19 pages, 1372 KiB

Open AccessArticle

Assessing CFTR Function and Epithelial Morphology in Human Nasal Respiratory Cell Cultures: A Combined Immunofluorescence and Electrophysiological Study

by Roshani Narayan Singh, Vanessa Mete, Willy van Driessche, Heymut Omran, Wolf-Michael Weber and Jörg Grosse-Onnebrink

Int. J. Mol. Sci. 2025, 26(15), 7618; https://doi.org/10.3390/ijms26157618 - 6 Aug 2025

Abstract

Cystic fibrosis (CF), the most common hereditary lung disease in Caucasians, is caused by dysfunction of the cystic fibrosis transmembrane conductance regulator (CFTR). We evaluated CFTR function using a newly developed Ussing chamber system, the Multi Trans Epithelial Current Clamp (MTECC), in an [...] Read more.

Cystic fibrosis (CF), the most common hereditary lung disease in Caucasians, is caused by dysfunction of the cystic fibrosis transmembrane conductance regulator (CFTR). We evaluated CFTR function using a newly developed Ussing chamber system, the Multi Trans Epithelial Current Clamp (MTECC), in an in vitro model of human airway epithelia. Air–liquid interface (ALI) cultures were established from nasal brushings of healthy controls (HC) and CF patients with biallelic CFTR variants. ALI layer thickness was similar between groups (HC: 62 ± 13 µm; CF: 55 ± 9 µm). Immunofluorescence showed apical CFTR expression in HC, but reduced or absent signal in CF cultures. MTECC enabled continuous measurement of transepithelial resistance (Rt), potential difference (PD), and conductance (G_t). G_t was significantly reduced in CF cultures compared to HC (0.825 ± 0.024 vs. −0.054 ± 0.016 mS/cm²), indicating impaired cAMP-inducible ion transport by CFTR. Treatment of CF cultures with elexacaftor, tezacaftor, and ivacaftor (Trikafta^®) increased G_t, reflecting partial restoration of CFTR function. These findings demonstrate the utility of MTECC in detecting functional differences in CFTR activity and support its use as a platform for evaluating CFTR-modulating therapies. Our model may contribute to the development of personalized treatment strategies for CF patients. Full article

(This article belongs to the Special Issue Molecular Mechanisms and Pathophysiology of Cystic Fibrosis)

29 pages, 5769 KiB

Open AccessArticle

Genetic Complexity in Spondyloarthritis: Contributions of HLA-B Alleles Beyond HLA-B*27 in Romanian Patients

by Ruxandra-Elena Nagit, Mariana Pavel-Tanasa, Corina Cianga, Elena Rezus and Petru Cianga

Int. J. Mol. Sci. 2025, 26(15), 7617; https://doi.org/10.3390/ijms26157617 - 6 Aug 2025

Abstract

This study examined the distribution and disease associations of non-HLA-B*27 HLA-B alleles in Romanian spondyloarthritis (SpA) patients, aiming to address the underrepresentation of Eastern European populations in immunogenetic research. Methods: We analyzed 263 HLA-B*27-negative patients from Northeastern Romania fulfilling ASAS criteria. HLA-B genotyping [...] Read more.

This study examined the distribution and disease associations of non-HLA-B*27 HLA-B alleles in Romanian spondyloarthritis (SpA) patients, aiming to address the underrepresentation of Eastern European populations in immunogenetic research. Methods: We analyzed 263 HLA-B*27-negative patients from Northeastern Romania fulfilling ASAS criteria. HLA-B genotyping was performed at two-digit resolution, and allele distributions were compared with two Romanian HLA-B*27-negative control groups (n = 335 and n = 1705 cases), using chi-square testing and logistic regression. Compared to controls, HLA-B*47 (p = 0.0007) and HLA-B*54 (p = 0.0013) were significantly enriched, while HLA-B*40 was underrepresented (p = 0.0287). Notably, HLA-B*54 was observed exclusively in axial SpA. Within the cohort, both HLA-B*13 and HLA-B*57 alleles were associated with psoriasis, while HLA-B*37 and HLA-B*41 alleles were clustered within the reactive arthritis group. The HLA-B*35 and HLA-B*18 alleles were the most frequently observed alleles across most clinical phenotypes. When comparing the frequency of HLA-B associations, the most common genotypes among SpA patients were B*08-B*18, B*13-B*35, and B*35-B*51. Notably, B*08-B*18 was more frequent in patients with radiographic sacroiliitis grade ≥ 2, while B*35-B*51 was more frequent in those with confirmed systemic inflammation, as indicated by elevated CRP or ESR levels. Analysis of peptide-binding patterns revealed a cluster of risk alleles, HLA-B*08, B*18, B*35, B*40, and B*54, sharing similar features, distinct from the canonical profile of B*27. These findings highlight the contribution of non-B*27 HLA-B alleles to SpA susceptibility in an Eastern European population and support the notion that HLA-B*27-negative SpA may represent a distinct clinical and immunological entity, driven by alternative pathogenic mechanisms. They also emphasize the importance of population-specific immunogenetic profiling and support expanding genetic characterization in HLA-B*27-negative patients. Full article

(This article belongs to the Special Issue Role of HLA (Human Leucocyte Antigen) in Human Diseases)

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31 pages, 4843 KiB

Open AccessReview

Glucocorticoid-Mediated Skeletal Muscle Atrophy: Molecular Mechanisms and Potential Therapeutic Targets

by Uttapol Permpoon, Jiyeong Moon, Chul Young Kim and Tae-gyu Nam

Int. J. Mol. Sci. 2025, 26(15), 7616; https://doi.org/10.3390/ijms26157616 - 6 Aug 2025

Abstract

Skeletal muscle atrophy is a critical health issue affecting the quality of life of elderly individuals and patients with chronic diseases. These conditions induce dysregulation of glucocorticoid (GC) secretion. GCs play a critical role in maintaining homeostasis in the stress response and glucose [...] Read more.

Skeletal muscle atrophy is a critical health issue affecting the quality of life of elderly individuals and patients with chronic diseases. These conditions induce dysregulation of glucocorticoid (GC) secretion. GCs play a critical role in maintaining homeostasis in the stress response and glucose metabolism. However, prolonged exposure to GC is directly linked to muscle atrophy, which is characterized by a reduction in muscle size and weight, particularly affecting fast-twitch muscle fibers. The GC-activated glucocorticoid receptor (GR) decreases protein synthesis and facilitates protein breakdown. Numerous antagonists have been developed to mitigate GC-induced muscle atrophy, including 11β-HSD1 inhibitors and myostatin and activin receptor blockers. However, the clinical trial results have fallen short of the expected efficacy. Recently, several emerging pathways and targets have been identified. For instance, GC-induced sirtuin 6 isoform (SIRT6) expression suppresses AKT/mTORC1 signaling. Lysine-specific demethylase 1 (LSD1) cooperates with the GR for the transcription of atrogenes. The kynurenine pathway and indoleamine 2,3-dioxygenase 1 (IDO-1) also play crucial roles in protein synthesis and energy production in skeletal muscle. Therefore, a deeper understanding of the complexities of GR transactivation and transrepression will provide new strategies for the discovery of novel drugs to overcome the detrimental effects of GCs on muscle tissues. Full article

(This article belongs to the Special Issue Understanding Aging in Health and Disease)

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14 pages, 3011 KiB

Open AccessArticle

Ameliorative Effects of Soybean Powder Fermented by Bacillus subtilis on Constipation Induced by Loperamide in Rats

by Gi Soo Lee, Su Kang Kim, Ju Yeon Ban and Chung-Hun Oh

Int. J. Mol. Sci. 2025, 26(15), 7615; https://doi.org/10.3390/ijms26157615 - 6 Aug 2025

Abstract

Constipation is a prevalent gastrointestinal disorder that significantly impairs quality of life. While pharmacological agents such as loperamide are widely used to induce constipation in experimental models, there is increasing interest in natural alternatives for alleviating intestinal dysfunction. In this study, we investigated [...] Read more.

Constipation is a prevalent gastrointestinal disorder that significantly impairs quality of life. While pharmacological agents such as loperamide are widely used to induce constipation in experimental models, there is increasing interest in natural alternatives for alleviating intestinal dysfunction. In this study, we investigated the laxative effects of soybean powder fermented by Bacillus subtilis DKU_09 in a loperamide-induced rat model of constipation. The probiotic strain was isolated from cheonggukjang, a traditional Korean fermented soybean paste, and its identity was confirmed through 16S rRNA sequencing. Fermented soybean powder was characterized morphologically via scanning electron microscopy and chemically via HPLC to assess its isoflavone content. Rats were administered loperamide (5 mg/kg) for four days to induce constipation and were then treated with fermented soybean powder at doses of 100, 200, or 300 mg/kg. No pharmacological laxatives (e.g., PEG) were used as a positive control; instead, values from the treatment groups were compared with those from the loperamide-only constipation group. Key outcomes of fecal output, water content, colonic fecal retention, and gastrointestinal transit ratio were measured. The fermented product significantly improved stool frequency and moisture content, reduced colonic fecal retention, and restored gastrointestinal transit in a dose-dependent manner. Notably, the 300 mg/kg group demonstrated nearly complete recovery of fecal parameters without affecting body weight. Statistical analysis was performed using one-way ANOVA followed by Tukey’s post hoc test. These findings suggest that Bacillus subtilis-fermented soybean powder exerts synergistic laxative effects through the combined action of probiotic viability and fermentation-enhanced bioactive compounds such as aglycone isoflavones. This study supports the potential use of fermented soybean-based nutraceuticals as a natural and safe intervention for constipation and gastrointestinal dysregulation. Full article

(This article belongs to the Special Issue Functions and Applications of Natural Products)

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14 pages, 1754 KiB

Open AccessArticle

Dissecting Tumor Heterogeneity by Liquid Biopsy—A Comparative Analysis of Post-Mortem Tissue and Pre-Mortem Liquid Biopsies in Solid Neoplasias

by Tatiana Mögele, Kathrin Hildebrand, Aziz Sultan, Sebastian Sommer, Lukas Rentschler, Maria Kling, Irmengard Sax, Matthias Schlesner, Bruno Märkl, Martin Trepel, Maximilian Schmutz and Rainer Claus

Int. J. Mol. Sci. 2025, 26(15), 7614; https://doi.org/10.3390/ijms26157614 - 6 Aug 2025

Abstract

Tumor heterogeneity encompasses genetic, epigenetic, and phenotypic diversity, impacting treatment response and resistance. Spatial heterogeneity occurs both inter- and intra-lesionally, while temporal heterogeneity results from clonal evolution. High-throughput technologies like next-generation sequencing (NGS) enhance tumor characterization, but conventional biopsies still do not adequately [...] Read more.

Tumor heterogeneity encompasses genetic, epigenetic, and phenotypic diversity, impacting treatment response and resistance. Spatial heterogeneity occurs both inter- and intra-lesionally, while temporal heterogeneity results from clonal evolution. High-throughput technologies like next-generation sequencing (NGS) enhance tumor characterization, but conventional biopsies still do not adequately capture genetic heterogeneity. Liquid biopsy (LBx), analyzing circulating tumor DNA (ctDNA), provides a minimally invasive alternative, offering real-time tumor evolution insights and identifying resistance mutations overlooked by tissue biopsies. This study evaluates the capability of LBx to capture tumor heterogeneity by comparing genetic profiles from multiple metastatic lesions and LBx samples. Eight patients from the Augsburger Longitudinal Plasma Study with various types of cancer provided 56 postmortem tissue samples, which were compared against pre-mortem LBx-derived circulating-free DNA sequenced by NGS. Tissue analyses revealed significant mutational diversity (4–12 mutations per patient, VAFs: 1.5–71.4%), with distinct intra- and inter-lesional heterogeneity. LBx identified 51 variants (4–17 per patient, VAFs: 0.2–31.1%), which overlapped with mutations from the tissue samples by 33–92%. Notably, 22 tissue variants were absent in LBx, whereas 18 LBx-exclusive variants were detected (VAFs: 0.2–2.8%). LBx effectively captures tumor heterogeneity, but should be used in conjunction with tissue biopsies for comprehensive genetic profiling. Full article

(This article belongs to the Special Issue Liquid Biopsies in Oncology—3rd Edition)

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18 pages, 2315 KiB

Open AccessArticle

Cannabinoid Receptors in the Horse Lateral Nucleus of the Amygdala: A Potential Target for Ameliorating Pain Perception, Stress and Anxiety in Horses

by Cristiano Bombardi, Giulia Salamanca, Claudio Tagliavia, Annamaria Grandis, Rodrigo Zamith Cunha, Alessandro Gramenzi, Margherita De Silva, Augusta Zannoni and Roberto Chiocchetti

Int. J. Mol. Sci. 2025, 26(15), 7613; https://doi.org/10.3390/ijms26157613 - 6 Aug 2025

Abstract

The amygdala is composed of several nuclei, including the lateral nucleus which is the main receiving area for the input from cortical and subcortical brain regions. It mediates fear, anxiety, stress, and pain across species. Evidence suggests that the endocannabinoid system may be [...] Read more.

The amygdala is composed of several nuclei, including the lateral nucleus which is the main receiving area for the input from cortical and subcortical brain regions. It mediates fear, anxiety, stress, and pain across species. Evidence suggests that the endocannabinoid system may be a promising target for modulating these processes. Cannabinoid and cannabinoid-related receptors have been identified in the amygdala of rodents, carnivores, and humans, but not in horses. This study aimed to investigate the gene expression of cannabinoid receptors 1 (CB1R) and 2 (CB2R), transient receptor potential vanilloid 1 (TRPV1), and peroxisome proliferator-activated receptor gamma (PPARγ) within the lateral nucleus of six equine amygdalae collected post mortem from an abattoir using quantitative real-time PCR, cellular distribution, and immunofluorescence. mRNA expression of CB1R and CB2R, but not TRPV1 or PPARγ, was detected. The percentage of immunoreactivity (IR) was calculated using ImageJ software. Cannabinoid receptor 1 immunoreactivity was absent in the somata but was strongly detected in the surrounding neuropil and varicosities and CB2R-IR was observed in the varicosities; TRPV1-IR showed moderate expression in the cytoplasm of somata and processes, while PPARγ-IR was weak-to-moderate in the neuronal nuclei. These findings demonstrate endocannabinoid system components in the equine amygdala and may support future studies on Cannabis spp. molecules acting on these receptors. Full article

(This article belongs to the Collection Feature Paper Collection in Molecular Endocrinology and Metabolism)

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18 pages, 3229 KiB

Open AccessArticle

AMPK-Targeting Effects of (−)-Epicatechin Gallate from Hibiscus sabdariffa Linne Leaves on Dual Modulation of Hepatic Lipid Accumulation and Glycogen Synthesis in an In Vitro Oleic Acid Model

by Hui-Hsuan Lin, Pei-Tzu Wu, Yu-Hsuan Liang, Ming-Shih Lee and Jing-Hsien Chen

Int. J. Mol. Sci. 2025, 26(15), 7612; https://doi.org/10.3390/ijms26157612 - 6 Aug 2025

Abstract

Metabolic dysfunction-associated steatotic liver disease (MASLD) begins with hepatic lipid accumulation and triggers insulin resistance. Hibiscus leaf extract exhibits antioxidant and anti-atherosclerotic activities, and is rich in (−)-epicatechin gallate (ECG). Despite ECG’s well-known pharmacological activities and its total antioxidant capacity being stronger than [...] Read more.

Metabolic dysfunction-associated steatotic liver disease (MASLD) begins with hepatic lipid accumulation and triggers insulin resistance. Hibiscus leaf extract exhibits antioxidant and anti-atherosclerotic activities, and is rich in (−)-epicatechin gallate (ECG). Despite ECG’s well-known pharmacological activities and its total antioxidant capacity being stronger than that of other catechins, its regulatory effects on MASLD have not been fully described previously. Therefore, this study attempted to evaluate the anti-MASLD potential of ECG isolated from Hibiscus leaves on abnormal lipid and glucose metabolism in hepatocytes. First, oleic acid (OA) was used as an experimental model to induce lipid dysmetabolism in human primary hepatocytes. Treatment with ECG can significantly (p < 0.05) reduce the OA-induced cellular lipid accumulation. Nile red staining revealed, compared to the OA group, the inhibition percentages of 29, 61, and 82% at the tested doses of ECG, respectively. The beneficial effects of ECG were associated with the downregulation of SREBPs/HMGCR and upregulation of PPARα/CPT1 through targeting AMPK. Also, ECG at 0.4 µM produced a significant (p < 0.01) decrease in oxidative stress by 83%, and a marked (p < 0.05) increase in glycogen synthesis by 145% on the OA-exposed hepatocytes with insulin signaling blockade. Mechanistic assays indicated lipid and glucose metabolic homeostasis of ECG might be mediated via regulation of lipogenesis, fatty acid β-oxidation, and insulin resistance, as confirmed by an AMPK inhibitor. These results suggest ECG is a dual modulator of lipid and carbohydrate dysmetabolism in hepatocytes. Full article

(This article belongs to the Special Issue Hepatopancreatic and Intestine Diseases: From Molecular Basis to Therapy)

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