Current Issues in Molecular Biology

10 pages, 4789 KiB

Open AccessCase Report

Partial Remission Without Recurrence in a 9-Year-Old Golden Retriever with Nasal Carcinoma Treated with Prednisolone/Chlorambucil Metronomic Combination Therapy: A Case Report and Literature Review of Molecular Mechanisms

by Kyuhyung Choi

Curr. Issues Mol. Biol. 2025, 47(8), 660; https://doi.org/10.3390/cimb47080660 - 15 Aug 2025

Abstract

This paper reports the first case in which a hyperlipidemic retriever (due to hypothyroidism) with a nasal tumor was successfully treated—achieving partial remission—and managed using a metronomic combination of chlorambucil (3.74 mg/m², SID) and prednisolone (0.28 mg/kg, SID) orally for 9 [...] Read more.

This paper reports the first case in which a hyperlipidemic retriever (due to hypothyroidism) with a nasal tumor was successfully treated—achieving partial remission—and managed using a metronomic combination of chlorambucil (3.74 mg/m², SID) and prednisolone (0.28 mg/kg, SID) orally for 9 months at a general practice. A 35 kg spayed female golden retriever aged 8 years and 8 months with nosebleeds visited the Bundang New York Animal Hospital in July 2023 after being diagnosed with nasal carcinoma. A protocol of 4 weeks of chemotherapy followed by 1 week of rest was repeated in two cycles and continued metronomically for 9 months without pause after the two cycles. The nasal exudate was significantly reduced. The size of the nasal tumor was monitored using computed tomography (CT) imaging at a referral hospital. Since the first occurrence of epistaxis, 18 months have passed (as of January 2025) and the nasal exudate is barely visible, and the vital signs and weight of the dog remain stable. The size of the nasal tumor significantly decreased after 9 months of chemotherapy completion without moderate side effects, and all the blood work was normalized, including hypercholesteremia. This study demonstrates that, in hyperlipidemic cancer patients, a prednisolone/chlorambucil metronomic combination which is cost-effective can be an alternative to tyrosine kinase inhibitors such as sorafenib, even when excluding the price. Through a literature review, the author also investigates the effect of the hyperlipidemic state on cancer, focusing on carcinoma and vascular endothelial growth factor (VEGF), as well as the RAS-RAF-MEK pathway, which is a target for tyrosine kinase inhibitors, in order to reveal the molecular mechanism of chlorambucil metronomic chemotherapy. Also, the author investigates the molecular pathway of carcinoma development in human hyperlipidemia patients through single-cell RNA sequence analysis using open public data, and discusses the molecular action of chlorambucil. Full article

(This article belongs to the Section Molecular Medicine)

28 pages, 1195 KiB

Open AccessReview

Targeting Intracellular Pathways in Atopic Dermatitis with Small Molecule Therapeutics

by Georgiana Nitulescu, Octavian Tudorel Olaru, Corina Andrei, George Mihai Nitulescu and Anca Zanfirescu

Curr. Issues Mol. Biol. 2025, 47(8), 659; https://doi.org/10.3390/cimb47080659 - 15 Aug 2025

Abstract

Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disorder characterized by immune dysregulation and epidermal barrier dysfunction. Advances in understanding the interplay of genetic predisposition, cytokine signaling, and environmental triggers have led to the emergence of targeted therapies. Although biologic agents such [...] Read more.

Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disorder characterized by immune dysregulation and epidermal barrier dysfunction. Advances in understanding the interplay of genetic predisposition, cytokine signaling, and environmental triggers have led to the emergence of targeted therapies. Although biologic agents such as dupilumab, tralokinumab, and lebrikizumab have revolutionized AD management, their high costs, injectable administration, and limited global accessibility highlight the need for alternative options. Small molecule therapies are gaining momentum as they target intracellular pathways central to AD pathogenesis and offer oral or topical administration routes. This review provides a comprehensive analysis of key agents including Janus kinase (JAK) inhibitors (upadacitinib, abrocitinib, baricitinib, ruxolitinib, delgocitinib), phosphodiesterase 4 (PDE4) inhibitors (crisaborole, difamilast, roflumilast, apremilast), as well as STAT6 degraders (KT621, NX3911), aryl hydrocarbon receptor modulators, histamine H4 receptor antagonists (adriforant, izuforant), and sphingosine-1-phosphate receptor modulators (etrasimod, BMS-986166). We summarize their mechanisms of action, pharmacological profiles, and pivotal clinical trial data, emphasizing their potential to address unmet therapeutic needs. Finally, we discuss safety concerns, long-term tolerability, and future directions for integrating small molecule therapies into precision treatment strategies for moderate-to-severe AD. Full article

(This article belongs to the Special Issue Novel Drugs and Natural Products Discovery)

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26 pages, 5444 KiB

Open AccessArticle

Exploring Novel Inhibitory Compounds Against Phosphatase Gamma 2: A Therapeutic Target for Male Contraceptives

by Hashim M. Aljohani, Bayan T. Bokhari, Alaa M. Saleh, Areej Yahya Alyahyawi, Renad M. Alhamawi, Mariam M. Jaddah, Mohammad A. Alobaidy and Alaa Abdulaziz Eisa

Curr. Issues Mol. Biol. 2025, 47(8), 658; https://doi.org/10.3390/cimb47080658 - 15 Aug 2025

Abstract

Men have limited options for contraception, despite the widely accepted public health benefits of it, placing the contraceptive burden solely on women. The current study focuses on inhibiting the PP1γ2 enzyme, which plays a role in sperm maturation and motility. The study considered [...] Read more.

Men have limited options for contraception, despite the widely accepted public health benefits of it, placing the contraceptive burden solely on women. The current study focuses on inhibiting the PP1γ2 enzyme, which plays a role in sperm maturation and motility. The study considered three top compounds based on the findings of molecular docking. The three compounds exhibited a good interaction profile with a binding affinity score of D751-0223 (−8.7 kcal/mol), D751-014 (−8.1 kcal/mol), and N117-0087 (−8 kcal/mol) measured in kcal/mol. Molecular dynamics simulation (MDS) were performed on the PP1γ2–ligand complexes along with the Apo form. The results suggested that all the complexes were stable with no major deviations observed compared to Apo. The average RMSDs for PP1γ2-D751-0223, D751-014, and Apo were 1.27 Å, 1.73 Å, 1.39 Å, and 1.69 Å, respectively. The PP1γ2–ligand complexes were observed with unique salt bridge interactions such as Glu133-Arg137, Asp4-Lys107, Asp188-Arg116, and Glu120-Arg90. The principal component analysis (PCA) findings indicated that every complex had a distinctive motion state. Furthermore, the net MM/PBSA scores for D751-0223, D751-0143, and N117-0087 were −80.01 kcal/mol, −72.18 kcal/mol, and −64.26 kcal/mol, respectively, while the MM/GBSA and MM/PBSA values were −82, −73.07,−67.26 and −80.01, −72.18, −64.26, measured in kcal/mol, respectively. The WaterSwap energy estimation was performed to validate the former technique, and the findings demonstrated that PP1γ2-D751-0223 is a stable complex, with a value of −51.05 kcal/mol. This work provides a baseline to researchers for the identification of novel therapeutic approaches for non-hormonal male contraceptives. Full article

(This article belongs to the Special Issue Harnessing Genomic Data for Disease Understanding and Drug Discovery)

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19 pages, 1906 KiB

Open AccessReview

The Duodenum-Centered Neurohormonal Hypothesis of Type 2 Diabetes: A Mechanistic Review and Therapeutic Perspective

by Athena N. Kapralou, Christos Yapijakis and George P. Chrousos

Curr. Issues Mol. Biol. 2025, 47(8), 657; https://doi.org/10.3390/cimb47080657 - 14 Aug 2025

Abstract

Type 2 diabetes mellitus (T2DM) is a multifactorial disorder defined by insulin resistance, β-cell dysfunction, and chronic hyperglycemia. Although peripheral mechanisms have been extensively studied, increasing evidence implicates the gastrointestinal tract in disease onset. Insights from bariatric surgery, gut hormone signaling, and incretin-based [...] Read more.

Type 2 diabetes mellitus (T2DM) is a multifactorial disorder defined by insulin resistance, β-cell dysfunction, and chronic hyperglycemia. Although peripheral mechanisms have been extensively studied, increasing evidence implicates the gastrointestinal tract in disease onset. Insights from bariatric surgery, gut hormone signaling, and incretin-based therapies suggest that the gut contributes actively beyond nutrient absorption. Yet, a cohesive framework integrating these observations remains absent, leaving a critical gap in our understanding of T2DM’s upstream pathophysiology. This work builds upon the anti-incretin theory, which posits that nutrient-stimulated neurohormonal signals—termed “anti-incretins”—arise from the proximal intestine to counteract incretin effects and regulate glycemic homeostasis. The excess of anti-incretin signals, perhaps stimulated by macronutrient composition or chemical additives of modern diets, disrupts this balance and may cause insulin resistance and β-cell depletion, leading to T2D. We hypothesize that the neuroendocrine signals produced by cholecystokinin (CCK)-I and secretin-S cells, both located in the proximal intestine, function as endogenous anti-incretins. In this context, we hypothesize a novel model centered on the chronic overstimulation of I and S cells by high-fat, high glycemic index modern diets. This drives what we term “amplified digestion”—a state marked by heightened vagal and hormonal stimulation of biliary and pancreatic secretions, increased enzymatic and bile acid activity, and alterations in bile acid composition. This condition leads to an extended breakdown of carbohydrates, lipids, and proteins into absorbable units, thereby promoting excessive nutrient absorption and ultimately contributing to insulin resistance and progressive β-cell failure. Multiple lines of clinical, surgical, and experimental evidence converge to support our model, rooted in the physiology of digestion and absorption. Western dietary patterns appear to induce an over-digestive adaptation—marked by excessive vagal and hormonal stimulation of biliary and pancreatic secretion—which amplifies digestive signaling. This heightened state correlates with increased nutrient absorption, insulin resistance, and β-cell dysfunction. Interventions that disrupt this maladaptive signaling—such as truncal vagotomy combined with duodenal bypass—may offer novel, physiology-based strategies for T2DM treatment. This hypothesis outlines a potential upstream contributor to insulin resistance and T2DM, grounded in digestive tract-derived neurohormonal dysregulation. This gut-centered model may provide insight into early, potentially reversible stages of the disease and identify a conceptual therapeutic target. Nonetheless, both the hypothesis and the accompanying surgical strategy—truncal vagotomy combined with proximal intestinal bypass—remain highly exploratory and require systematic validation through mechanistic and clinical studies. Further investigation is warranted to clarify the molecular regulation of I and S enteroendocrine cells, including the genetic and epigenetic factors that may drive hypersecretion. While speculative, interventions—surgical or pharmacologic—designed to modulate these digestive signals could represent a future avenue for research into T2DM prevention or remission, pending rigorous evidence. Full article

(This article belongs to the Special Issue Molecular Insights into Multifactorial Causes of Insulin Resistance in Obesity)

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10 pages, 1645 KiB

Open AccessArticle

Molecular Characterization of Citrus Accessions Grown for Pre-Breeding Purposes

by Israel Felipe Gonçalves Soares, Felipe Cruz Paula, Conceição de Maria Batista Oliveira, José Dias de Souza Neto, Talles de Oliveira Santos, Rafael Nunes de Almeida, Ana Paula Candido Gabriel Berilli, Sávio da Silva Berilli, Taís Cristina Bastos Soares, Jardel Oliveira Santos, Alexandre Cristiano Santos Júnior and Monique Moreira Moulin

Curr. Issues Mol. Biol. 2025, 47(8), 656; https://doi.org/10.3390/cimb47080656 - 14 Aug 2025

Abstract

The objective of this work was to analyse the genetic diversity of a population of Citrus spp. in the south of the State of Espírito Santo, Brazil, for pre-breeding studies. For that, a total of sixty genotypes were analysed, including ten citrus varieties [...] Read more.

The objective of this work was to analyse the genetic diversity of a population of Citrus spp. in the south of the State of Espírito Santo, Brazil, for pre-breeding studies. For that, a total of sixty genotypes were analysed, including ten citrus varieties from four species of the Citrus genus. The methodology involved DNA extraction, amplification via polymerase chain reaction, and the use of a set of 16 Simple Sequence Repeat markers. These markers identified 42 alleles, with a variation of one to four alleles per locus, an average heterozygosity value of 0.53, and an average polymorphic information content of up to 0.29 per species. After the analysis, a dissimilarity matrix was generated using Jaccard distance and a dendrogram, revealing the formation of two groups: Group I, comprising Citrus sinensis varieties, and Group II, comprising varieties of Citrus latifolia, Citrus aurantifolia, and Citrus reticulata. Our study demonstrated that the combination of these markers allowed for the differentiation of genotypes within the collection. The results obtained are valuable for the future management of the collection and the efficient use of genetic diversity estimation in Citrus spp. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants, 2nd Edition)

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35 pages, 2758 KiB

Open AccessReview

Redox Homeostasis in Red Blood Cells: From Molecular Mechanisms to Antioxidant Strategies

by Sara Spinelli, Angela Marino, Alessia Remigante and Rossana Morabito

Curr. Issues Mol. Biol. 2025, 47(8), 655; https://doi.org/10.3390/cimb47080655 - 14 Aug 2025

Abstract

Red blood cells (RBCs) are uniquely vulnerable to oxidative stress due to their role in O₂ transport and their high content of heme iron and polyunsaturated fatty acids (PUFAs). Despite lacking nuclei and organelles, RBC homeostasis relies on a finely tuned redox [...] Read more.

Red blood cells (RBCs) are uniquely vulnerable to oxidative stress due to their role in O₂ transport and their high content of heme iron and polyunsaturated fatty acids (PUFAs). Despite lacking nuclei and organelles, RBC homeostasis relies on a finely tuned redox system to preserve membrane integrity, cytoskeletal organization, and metabolic function. Impairment of this delicate balance results in a series of oxidative events that ultimately leads to the premature clearance of RBCs from the bloodstream. This review outlines the main oxidative mechanisms that affect RBC at different levels, such as membrane, cytoskeleton, and intracellular environment, with a focus on the molecular targets of reactive species. The role of major antioxidant systems in preventing or reversing redox damage will also be examined, revealing their multiple mechanisms of action ranging from direct ROS scavenging to the enhancement of endogenous antioxidant defense pathways. Redox regulatory mechanisms in RBCs are required to maintain membrane integrity, cytoskeletal organization, and metabolic function. Disruption of these processes causes several oxidative processes that trigger premature RBC removal. Cumulative evidence places oxidative stress at the core of RBC dysfunction in both physiological aging and pathological conditions, including diabetes, inflammatory conditions, and hemolytic disorders. Antioxidant-based strategies, rather than providing generalized protection, should aim to selectively target the specific molecular pathways affected in distinct clinical settings. Full article

(This article belongs to the Special Issue Therapeutic Effects of Natural Bioactive Compounds in the Management of Human Diseases)

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23 pages, 1140 KiB

Open AccessReview

Hypersensitivity to Folic Acid and/or Folinic Acid—A Review of Clinical Cases, Potential Mechanism, Possible Cross-Allergies and Current Diagnostic Options

by Kinga Lis

Curr. Issues Mol. Biol. 2025, 47(8), 654; https://doi.org/10.3390/cimb47080654 - 14 Aug 2025

Abstract

Folic acid and its derivatives (e.g., folinic acid) are a group of water-soluble compounds collectively known as vitamin B9. Synthetic folic acid is a component of dietary supplements, medications and other pharmaceuticals and fortified foods. Folinic acid (5-formyltetrahydrofolic acid) is the active metabolite [...] Read more.

Folic acid and its derivatives (e.g., folinic acid) are a group of water-soluble compounds collectively known as vitamin B9. Synthetic folic acid is a component of dietary supplements, medications and other pharmaceuticals and fortified foods. Folinic acid (5-formyltetrahydrofolic acid) is the active metabolite of folic acid. It is used to treat vitamin B9 deficiency and as an adjunct to various combination therapies. Hypersensitivity reactions to folic acid or folinic acid are rare and occur following exposure to synthetic folic acid or its derivatives but not on natural folates. In people allergic to folates, cross-reactions are possible following exposure to folic acid analogues (including antifolates, e.g., methotrexate). The mechanism of hypersensitivity to folic acid and/or folinic acid has not been clearly established. Both IgE-dependent and non-IgE-dependent hypersensitivity reactions are likely. It is possible that folic or folinic acid is either an immunogen or a hapten. Diagnosing hypersensitivity to folic/folinic acid is difficult. There are no validated in vitro or in vivo diagnostic tests. The basophil activation test (BAT) appears to be a promising tool for diagnosing folate allergy. The aims of the manuscript were to review published clinical cases of hypersensitivity reactions to folic or folinic acid, potential mechanisms of these reactions and possible cross-allergies, and current diagnostic possibilities of folate hypersensitivity. Full article

(This article belongs to the Special Issue Molecular Mechanisms and Regulation in Allergy and Immune Diseases, Immunodeficiencies, 2nd Edition)

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27 pages, 1370 KiB

Open AccessReview

Immune Organoids: A Review of Their Applications in Cancer and Autoimmune Disease Immunotherapy

by David B. Olawade, Emmanuel O. Oisakede, Eghosasere Egbon, Saak V. Ovsepian and Stergios Boussios

Curr. Issues Mol. Biol. 2025, 47(8), 653; https://doi.org/10.3390/cimb47080653 - 13 Aug 2025

Abstract

Immune organoids have emerged as a ground-breaking platform in immunology, offering a physiologically relevant and controllable environment to model human immune responses and evaluate immunotherapeutic strategies. Derived from stem cells or primary tissues, these three-dimensional constructs recapitulate key aspects of lymphoid tissue architecture, [...] Read more.

Immune organoids have emerged as a ground-breaking platform in immunology, offering a physiologically relevant and controllable environment to model human immune responses and evaluate immunotherapeutic strategies. Derived from stem cells or primary tissues, these three-dimensional constructs recapitulate key aspects of lymphoid tissue architecture, cellular diversity, and functional dynamics, providing a more accurate alternative to traditional two-dimensional cultures and animal models. Their ability to mimic complex immune microenvironments has positioned immune organoids at the forefront of cancer immunotherapy development, autoimmune disease modeling, and personalized medicine. This narrative review highlights the advances in immune organoid technology, with a focus on their applications in testing immunotherapies, such as checkpoint inhibitors, CAR-T cells, and cancer vaccines. It also explores how immune organoids facilitate the study of autoimmune disease pathogenesis with insights into their molecular basis and support in high-throughput drug screening. Despite their transformative potential, immune organoids face significant challenges, including the replication of systemic immune interactions, standardization of fabrication protocols, scalability limitations, biological heterogeneity, and the absence of vascularization, which restricts organoid size and maturation. Future directions emphasize the integration of immune organoids with multi-organ systems to better replicate systemic physiology, the development of advanced biomaterials that closely mimic lymphoid extracellular matrices, the incorporation of artificial intelligence (AI) to optimize organoid production and data analysis, and the rigorous clinical validation of organoid-derived findings. Continued innovation and interdisciplinary collaboration will be essential to overcome existing barriers, enabling the widespread adoption of immune organoids as indispensable tools for advancing immunotherapy, vaccine development, and precision medicine. Full article

(This article belongs to the Section Molecular Medicine)

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24 pages, 11598 KiB

Open AccessArticle

Integrating Primary and Metastatic scRNA–Seq and Bulk Data to Develop an Immune–Based Prognosis Signature for Colorectal Cancer

by Kaiyuan Xing, Liangshuang Li, Yingnan Ma and Jiang Zhu

Curr. Issues Mol. Biol. 2025, 47(8), 652; https://doi.org/10.3390/cimb47080652 - 13 Aug 2025

Abstract

Colorectal cancer (CRC) is a highly aggressive cancer, with its treatment and prognosis particularly challenging due to metastasis. The immune response is involved in the whole process of CRC development, and immunotherapy has increasingly become a part of CRC patients’ treatment. However, comprehensive [...] Read more.

Colorectal cancer (CRC) is a highly aggressive cancer, with its treatment and prognosis particularly challenging due to metastasis. The immune response is involved in the whole process of CRC development, and immunotherapy has increasingly become a part of CRC patients’ treatment. However, comprehensive research on the immune microenvironment driving CRC metastasis remains limited. Given this limitation, we proposed a bioinformatics method to construct a metastasis–based immune prognostic model (MIPM) by integrating CRC single–cell RNA sequencing (scRNA–seq) and bulk data. Our study identified several MIPM genes significantly associated with CRC metastasis and progression. MIPM reliably predicted overall survival (OS) and tumor recurrence in CRC across eleven bulk validation datasets. Notably, MIPM could independently predict outcomes beyond traditional clinical factors such as age, sex, and stage. It showed high predictive accuracy in CRC patients treated with chemotherapy. Drug sensitivity and multifaceted immune analyses further underscored the importance of MIPM in therapeutic and immunotherapy response modulation. In conclusion, our findings have profound implications for the illustration of MIPM, which could serve as a new plausible prognostic marker for CRC patients and provide new insights for treatment strategies. The further evaluation and investigation of MIPM will enhance the prognosis and precision therapy of CRC patients. Full article

(This article belongs to the Section Bioinformatics and Systems Biology)

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17 pages, 1885 KiB

Open AccessArticle

BCG Impact on PD-1/PD-L1 Expression in Peripheral Immunocytes of Cancer Patients—A Potential Explanation for Its Activity in Preventing Alzheimer’s Disease

by Benjamin Y. Klein, Ofer N. Gofrit and Charles L. Greenblatt

Curr. Issues Mol. Biol. 2025, 47(8), 651; https://doi.org/10.3390/cimb47080651 - 13 Aug 2025

Abstract

We found, retrospectively, that BCG therapy in non-muscle invasive bladder cancer (NMIBC) reduces the rate of Alzheimer’s disease. Blockade of the ligand PD-L1 or its checkpoint receptor PD-1 has been shown to improve cognitive function and reduce brain pathology features in a mouse [...] Read more.

We found, retrospectively, that BCG therapy in non-muscle invasive bladder cancer (NMIBC) reduces the rate of Alzheimer’s disease. Blockade of the ligand PD-L1 or its checkpoint receptor PD-1 has been shown to improve cognitive function and reduce brain pathology features in a mouse model of Alzheimer’s disease (AD). Given that peripheral blood mononuclear cells (PBMCs) are involved in aging brain pathology and thus represent a potential AD therapeutic target, we analyzed the impact of BCG on the expression of PD-1, PD-L1, and inflammation modulators in PBMCs. Cryopreserved PBMCs pre- and post-BCG-treated six melanoma and six NMIBC patients were repurposed for immunoelectrophoretic analysis of PBMC-extracted proteins. PBMCs, post-BCG treatment in melanoma patients, were harvested only 4 months after the start of treatment (short BCG period), whereas the PBMCs of NMIBC patients were harvested 24 to 52 months after starting the BCG treatment. In melanoma PBMCs, BCG upregulated PD-L1 (p = 0.052) while downregulating PD-1 (insignificantly, p = 0.16). In contrast, in NMIBC patients, BCG downregulated PD-L1 (insignificantly, p = 0.67), while upregulating PD-1 (p = 0.0082). PD-L1 positive correlation with p-IkB (r = 0.7228) under BCG is inverted to that of PD-L1 against IkB (p = −0.9491). The difference between these opposite correlations is significant (p = 0.011), indicating that PD-L1 is upregulated early after BCG treatment, in association with p-IKB, which enables inflammation. This association subsided later, and for PD-1, did not occur at the short or long BCG periods. Experiments with a larger number of patients may substantiate the hypothesis that an increase in PD-1 by BCG relative to PD-L1 may protect against AD. Full article

(This article belongs to the Special Issue Cellular and Molecular Biology Insights into Neurodegenerative Diseases: From Pathogenesis to Therapeutic Targets)

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17 pages, 2011 KiB

Open AccessReview

A Narrative Review of Heavy Metals and Sperm Quality: The Interplay with Antioxidant Imbalance and Reactive Oxygen Species

by Soukaina Azil, Khaoula Errafii, Moncef Benkhalifa, Noureddine Louanjli, Bouchra Ghazi and Salsabil Hamdi

Curr. Issues Mol. Biol. 2025, 47(8), 650; https://doi.org/10.3390/cimb47080650 - 13 Aug 2025

Abstract

Reproductive infertility is characterized by the inability to achieve pregnancy after a year or more of unprotected sexual intercourse. This review highlights the significant impact of exposure to both types of heavy metals (essential and non-essential) on the reproductive performance of various species, [...] Read more.

Reproductive infertility is characterized by the inability to achieve pregnancy after a year or more of unprotected sexual intercourse. This review highlights the significant impact of exposure to both types of heavy metals (essential and non-essential) on the reproductive performance of various species, particularly humans. Heavy metals present a high atomic density and weight, including lead, mercury, cadmium, nickel, chromium, and arsenic, and are delivered into the environment through natural and human activities, posing a threat to ecological systems and human reproductive health. These heavy metals have the potential for bioaccumulation and can adversely affect male fertility and sperm quality due to their role in disrupting endocrine functions, altering hormone levels responsible for sperm production, and inducing oxidative stress. The elevated production of reactive oxygen species (ROS) exceeds the capability of antioxidants and can lead to the alteration of sperm quality. Seminal fluid contains antioxidants like vitamin C, vitamin E, zinc, and selenium to counteract the impacts of ROS and also to preserve the sperm function. This review aims also to explore the impact of heavy metals on sperm quality and their relationship with antioxidant imbalance and ROS. The exposure to heavy metals whether through occupational or environmental means increases the production of ROS and therefore leads to an imbalance of antioxidants production. All these factors have no doubt an impact on male reproductive health. Full article

(This article belongs to the Special Issue Latest Review Papers in Molecular Biology 2025)

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21 pages, 3063 KiB

Open AccessArticle

Evaluation of the Safety and Antiproliferative Activity of Bulgarian Rose Essential Oil: An In Vitro and In Silico Model of Colorectal Adenocarcinoma

by Rayna Nenova, Kalin Kalinov, Deyana Nedeva, Ana Dobreva, Neli Vilhelmova-Ilieva, Ani Georgieva and Ivan Iliev

Curr. Issues Mol. Biol. 2025, 47(8), 649; https://doi.org/10.3390/cimb47080649 - 13 Aug 2025

Abstract

The side effects of conventional cancer treatments, such as chemotherapy, radiotherapy, etc., worsen the quality of life of patients. Therefore, it is necessary to explore the possibilities of creating new drugs containing natural products with low toxicity. The experimental scientific pharmacological research of [...] Read more.

The side effects of conventional cancer treatments, such as chemotherapy, radiotherapy, etc., worsen the quality of life of patients. Therefore, it is necessary to explore the possibilities of creating new drugs containing natural products with low toxicity. The experimental scientific pharmacological research of rose preparations in Bulgaria began in the first half of the 20th century. Bulgarian rose essential oil (BREO) is qualified by GC FID analysis. To study the effect of the BREO, we used HCT-8 and HT-29 tumor cell lines. As a model of healthy tissue, we used the non-tumorigenic cells MCF-12F. Cells were treated with twofold increasing concentrations of BREO from 7.5 µg/mL to 1000 µg/mL. The NRU test and MTT assay were used for evaluation of the safety, antiproliferative activity and colony formation assay. Our results showed low cytotoxicity (CC₅₀ = 629.72 ± 22.38 μg/mL) and high level of photosafety (PIF = 0.92) of BREO. The antiproliferative activity test shows that the BREO has an IC₅₀ = 290.45 ± 10.79 μg/mL for the HT-29 cells. In the normal cell line MCF-12F, this effect is lower (IC₅₀ = 383.90 ± 34.75 μg/mL). Furthermore, colony forming assay showed a significant reduction in IC₅₀ value (IC₅₀ = 163.79 ± 10.25 μg/mL) in HT-29 cells. The in silico experiments confirmed the potential of the BREO for antiproliferative effect and further activation of different pathways leading to apoptosis. Full article

(This article belongs to the Special Issue The Green Revolution in Cancer Research: Bioactive Substances from Plants as Promising Therapeutics)

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17 pages, 1715 KiB

Open AccessArticle

Biochemical Changes in Prostate Cancer: FMNL1 and PAK1 in Plasma and Urine

by Elif Bilgin Doğru, Selçuk Erdem, Hilal Oğuz Soydinç, Ayça İribaş and Derya Duranyıldız

Curr. Issues Mol. Biol. 2025, 47(8), 648; https://doi.org/10.3390/cimb47080648 - 13 Aug 2025

Abstract

Prostate cancer is a clinically heterogeneous disease. Since PSA is not cancer-specific, and due to the bone metastases seen in the advanced stage and bone deformations caused by hormone therapy, it is necessary to use new biomarkers. Formin-like-protein 1 (FMNL1), a member of [...] Read more.

Prostate cancer is a clinically heterogeneous disease. Since PSA is not cancer-specific, and due to the bone metastases seen in the advanced stage and bone deformations caused by hormone therapy, it is necessary to use new biomarkers. Formin-like-protein 1 (FMNL1), a member of the formin protein family, is of great importance in actin polymerization, cell attachment, and migration processes. p21-activated kinase 1 (PAK1) proteins, members of the PAK protein kinases, play a role in cytoskeletal organization, as well as regulating other cellular activities such as cell survival, mitosis, and transcription. In our study, plasma and urine samples of 60 prostate cancer patients and 20 healthy controls were studied using RT-PCR and ELISA methods. No statistical difference was found between FMNL1 mRNA and protein expression levels of patients and controls in both plasma and urine samples (p > 0.05). There was no statistical difference between PAK1 mRNA expression levels of patients and controls in plasma and urine samples (p > 0.05). While no significant difference was found in PAK1 protein levels in plasma samples (p > 0.05), it was found to be lower in urine samples of patients compared to the control group (p = 0.00). Both marker molecules have low expression levels in early-stage PCa. Full article

(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)

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23 pages, 1316 KiB

Open AccessReview

Can Salivary Biomarkers Serve as Diagnostic and Prognostic Tools for Early Detection in Patients with Colorectal Cancer? A Systematic Review

by Stanisław Krokosz, Maria Obrycka and Anna Zalewska

Curr. Issues Mol. Biol. 2025, 47(8), 647; https://doi.org/10.3390/cimb47080647 - 12 Aug 2025

Abstract

Colorectal cancer (CRC) stands as one of the most prevalent and lethal forms of cancer worldwide with early detection playing a crucial role in improving the survival rate. Salivary biomarkers have emerged as a promising non-invasive alternative for CRC early detection. A comprehensive [...] Read more.

Colorectal cancer (CRC) stands as one of the most prevalent and lethal forms of cancer worldwide with early detection playing a crucial role in improving the survival rate. Salivary biomarkers have emerged as a promising non-invasive alternative for CRC early detection. A comprehensive search of the Web of Science, Scopus, and PubMed databases was performed to identify relevant studies published between 2018 and April 2025. Inclusion criteria focused on studies analyzing salivary biomarkers in adult CRC patients, while pediatric studies, non-diagnostic applications, and studies with insufficient statistical power were excluded. A total of 12 studies were included in this review, identifying various salivary biomarkers associated with CRC. Salivary microbiota, including Fusobacterium nucleatum and other bacterial species, demonstrated potential as diagnostic markers. Metabolomic profiling revealed elevated levels of lactate and pyruvate, reflecting metabolic alterations in CRC. Several microRNAs, such as miR-92a and miR-29a, exhibited high sensitivity and specificity for CRC detection. Additionally, protein-based biomarkers, including chemerin and sHLA-G, were found to be significantly elevated in CRC patients. Salivary biomarkers show great promise as a non-invasive, cost-effective approach for CRC detection and prognosis. Their ability to reflect systemic disease processes makes them a valuable complement to existing screening methods. Full article

(This article belongs to the Section Molecular Medicine)

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12 pages, 2441 KiB

Open AccessArticle

Linolenic Acid Inhibits Cancer Stemness and Induces Apoptosis by Regulating Nrf2 Expression in Gastric Cancer Cells

by Jen-Lung Chen, Yi-Shih Ma, Kuen-Jang Tsai, Hsin-Yi Tsai, Li-Jen Yeh, Hung-Wen Tsai, Judy Yen, Hong-Wen Tsai and Ming-Wei Lin

Curr. Issues Mol. Biol. 2025, 47(8), 646; https://doi.org/10.3390/cimb47080646 - 12 Aug 2025

Abstract

Although chemotherapy is the preferred treatment for gastric cancer, the therapeutic drugs currently available have limited efficacy and severe side effects. Cancer stem cells within tumor masses have the distinctive properties of self-renewal, maintenance, and resistance to chemotherapy. Hence, agents capable of targeting [...] Read more.

Although chemotherapy is the preferred treatment for gastric cancer, the therapeutic drugs currently available have limited efficacy and severe side effects. Cancer stem cells within tumor masses have the distinctive properties of self-renewal, maintenance, and resistance to chemotherapy. Hence, agents capable of targeting stemness in gastric tumors with minimal side effects are urgently required. Enzymes that generate reactive oxygen species contribute to the high oxidation levels observed in tumors. Additionally, nuclear factor erythroid 2-related factor 2 (Nrf2), an antioxidant transcription factor, regulates cancer stemness. Increasing evidence highlights the potential of nutritional supplementation to treat cancer stemness. ω-3 polyunsaturated fatty acids support human health and offer benefits for cancer treatment. Linolenic acid (LA), an ω-3 polyunsaturated fatty acid, inhibits the expression of proteins associated with stemness and promotes apoptosis in gastric cancer cells. Our findings indicated that LA treatment substantially inhibited key characteristics of gastric cancer stemness and induced oxidative stress and caspase-3-mediated apoptosis by downregulating Nrf2-mediated expression. These results suggest that LA is a promising nutritional supplement for targeting cancer stemness in the treatment of gastric cancer. Full article

(This article belongs to the Special Issue Targeting Tumor Microenvironment for Cancer Therapy, 3rd Edition)

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14 pages, 4774 KiB

Open AccessReview

Biochemical Battle: Influence of Omega-6 Fatty Acids on the Formation of DNA Adducts with 4-HNE

by Edyta Błaszczyk and Bolesław T. Karwowski

Curr. Issues Mol. Biol. 2025, 47(8), 645; https://doi.org/10.3390/cimb47080645 - 12 Aug 2025

Abstract

While omega-6 fatty acids play an important role in normal cell function, their excess in the diet is associated with an increased risk of developing diseases such as obesity, non-alcoholic fatty liver disease (NAFLD), inflammatory bowel disease (IBD) and Alzheimer’s disease. Furthermore, excessive [...] Read more.

While omega-6 fatty acids play an important role in normal cell function, their excess in the diet is associated with an increased risk of developing diseases such as obesity, non-alcoholic fatty liver disease (NAFLD), inflammatory bowel disease (IBD) and Alzheimer’s disease. Furthermore, excessive intake has been shown to lead to chronic inflammation, which is related to increased production of reactive oxygen species (ROS). This conditioncan initiate lipid peroxidation in cell membranes, leading to the degradation of their fatty acids. One of the main products of omega-6 peroxidation is the α,β-unsaturated aldehyde, i.e., 4-hydroxynonenal (4-HNE), which is able to form four diastereoisomeric adducts with guanine. These 4-HNE adducts have been identified in the DNA of humans and rodents. Depending on their stereochemistry, they are able to influence double helix stability and cause DNA–DNA or DNA–Protein cross-links. Moreover, studies have shown that 4-HNE adducts formed in the human genome are considered mutation hotspots in hepatocellular carcinoma. Although the cell possesses defence mechanisms, without a well-balanced diet allowing correct cell function, they may not be sufficient to protect the genetic code. This review provides an overview of the molecular mechanisms underlying oxidative stress, lipid peroxidation, and the formation of DNA adducts. Particular emphasis is placed on the role of an omega-6-rich diet in inflammatory diseases, and on the formation of 4-HNE, which is a major product of lipid peroxidation, and its broader implications for genome stability, ageing, and disease progression. Full article

(This article belongs to the Special Issue Latest Review Papers in Molecular Biology 2025)

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16 pages, 8770 KiB

Open AccessArticle

Integrated Transcriptomic and Metabolomic Analyses Shed Light on the Regulation of Aromatic Amino Acid Biosynthesis in a Novel Albino Tea (Camellia sinensis) Mutation

by Ying Gao, Suimei Li, Xiaojia Zhang, Shuwei Yu, Xinyu Liu, Changbo Yuan, Yuantao Yao, Fan’an Zhang and Lubin Song

Curr. Issues Mol. Biol. 2025, 47(8), 644; https://doi.org/10.3390/cimb47080644 - 12 Aug 2025

Abstract

Off-white or yellowish shoots are common in tea plants (Camellia sinensis L.), and such albino variations are often accompanied by metabolic reprogramming, including increased contents of amino acids and lower levels of polyphenols. Nonetheless, the molecular mechanisms that underlie these albino variations [...] Read more.

Off-white or yellowish shoots are common in tea plants (Camellia sinensis L.), and such albino variations are often accompanied by metabolic reprogramming, including increased contents of amino acids and lower levels of polyphenols. Nonetheless, the molecular mechanisms that underlie these albino variations remain to be fully clarified. Here, we examined the ultrastructural characteristics of novel, naturally occurring, yellowish mutated tea leaves and performed metabolomic analyses on green and albino leaves and stems. Then, transcriptomic analyses were also conducted on green and albino leaves to investigate the mechanistic basis of the albino variation. As expected, the cells of albino tea leaves contained fewer and smaller chloroplasts with disorganized thylakoids and smaller starch granules. Widely targeted metabolomics analysis revealed 561 differentially abundant metabolites between green and albino leaves and stems, but there was little difference between green and albino stems. Then, RNA sequencing of green and albino leaves revealed downregulation of genes associated with light harvesting and photosynthesis, and integration of the metabolomic and transcriptomic results indicated that biosynthesis of aromatic amino acids (AAAs) was strongly upregulated in albino leaves. To gain additional insight into the molecular basis of the increased AAA levels, Oxford Nanopore long-read sequencing was performed on green and albino leaves, which enabled us to identify differences in long non-coding RNAs (lncRNAs) and alternatively spliced transcripts between green and albino leaves. Interestingly, the amino acid biosynthesis genes arogenate dehydratase/prephenate dehydratase (ADT) and serine hydroxymethyltransferase (SHMT) were highlighted in the lncRNA and alternative splicing analyses, and the transcription factor genes PLATZ, B3 Os04g0386900, and LRR RLK At1g56140 showed significant changes in both expression and alternative splicing in albino leaves. Together, our data suggest that biosynthesis of AAAs might be crucial for albino mutations in tea plants and could be coordinated with the regulation of lncRNAs and alternative splicing. This is a complex regulatory network, and further exploration of the extensive metabolic reprogramming of albino tea leaves will be beneficial. Full article

(This article belongs to the Special Issue Genetics and Natural Bioactive Components in Beverage Plants)

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29 pages, 12966 KiB

Open AccessArticle

Integrative Analysis of Differentially Expressed miRNAs and Noncoding RNA Networks Reveals Molecular Mechanisms Underlying Metritis in Postpartum Dairy Cows

by Ramanathan Kasimanickam, Joao Ferreira and Vanmathy Kasimanickam

Curr. Issues Mol. Biol. 2025, 47(8), 643; https://doi.org/10.3390/cimb47080643 - 11 Aug 2025

Abstract

Postpartum metritis in dairy cows compromises reproductive performance and leads to substantial economic losses. This study investigated the molecular mechanisms underlying metritis by integrating high-throughput circulating microRNA (miRNA) profiling with systems-level bioinformatics. Previously, 30 differentially expressed miRNAs, 16 upregulated and 14 downregulated, were [...] Read more.

Postpartum metritis in dairy cows compromises reproductive performance and leads to substantial economic losses. This study investigated the molecular mechanisms underlying metritis by integrating high-throughput circulating microRNA (miRNA) profiling with systems-level bioinformatics. Previously, 30 differentially expressed miRNAs, 16 upregulated and 14 downregulated, were identified in metritis-affected cows compared to healthy controls. Building on these findings, this study predicted miRNA target genes and constructed regulatory networks involving miRNAs, mRNAs, circRNAs, lncRNAs, and snRNAs, alongside protein–protein interaction networks. Functional annotation and KEGG pathway analysis revealed that upregulated miRNAs influenced genes involved in immune activation, apoptosis, and metabolism, while downregulated miRNAs were associated with angiogenesis, immune suppression, and tissue repair. Hub genes such as AKT3, VEGFA, and HIF1A were central to immune and angiogenic signaling, whereas UBE3A and ZEB1 were linked to immune inhibition. Interferon-stimulated genes (e.g., ISG15, RSAD2, CXCL chemokines) were shown to regulate solute carriers, contributing to immune dysregulation. Key pathways included PI3K-Akt, NF-κB, JAK-STAT, insulin resistance, and T cell receptor signaling. Noncoding RNAs such as NEAT1, KCNQ1OT1, and XIST, along with miRNAs like bta-miR-15b and bta-miR-148a, emerged as pro-inflammatory regulators, while bta-miR-199a-3p appeared to exert immunosuppressive effects. These findings offer new insights into the complex regulatory networks driving metritis and suggest potential targets for improving fertility in dairy cows. Full article

(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)

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16 pages, 2155 KiB

Open AccessArticle

Molecular Insights into Tumor Immunogenicity

by Irini Doytchinova, Stanislav Sotirov and Ivan Dimitrov

Curr. Issues Mol. Biol. 2025, 47(8), 641; https://doi.org/10.3390/cimb47080641 - 11 Aug 2025

Abstract

Tumor immunogenicity depends on the ability of peptides to form stable and specific interactions with both HLA molecules and T-cell receptors (TCRs). While HLA binding is essential, not all HLA-binding peptides elicit T-cell responses. This study investigates the molecular features distinguishing immunogenic T-cell [...] Read more.

Tumor immunogenicity depends on the ability of peptides to form stable and specific interactions with both HLA molecules and T-cell receptors (TCRs). While HLA binding is essential, not all HLA-binding peptides elicit T-cell responses. This study investigates the molecular features distinguishing immunogenic T-cell epitopes from non-immunogenic HLA binders. Two datasets of nonamer peptides—38 T-cell epitopes and 144 non-epitopes—were compiled and analyzed using sequence logo models and molecular dynamics (MD) simulations of TCR–peptide–HLA complexes. A comparative logo analysis revealed strong amino acid preferences at central positions (p4–p8) in T-cell epitopes and absences in non-epitopes. A representative epitope–non-epitope pair was selected for structural modeling and 100 ns MD simulations. The T-cell epitope formed a more stable complex with the TCR and exhibited greater flexibility, supporting an induced-fit recognition mechanism. It also established a broader and longer-lasting network of hydrogen bonds and π interactions across the residues at positions p4–p8. In contrast, the non-epitope engaged TCR at only two positions. These findings highlight the critical role of the peptide’s central region in TCR engagement and provide structural insights useful for neoantigen prediction, vaccine design, and TCR-based immunotherapies. Full article

(This article belongs to the Special Issue Molecular Biology in Drug Design and Precision Therapy)

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