Biomolecules

30 pages, 4229 KiB

Open AccessReview

Multifaceted Therapeutic Potential of Plant-Derived Exosomes: Immunomodulation, Anticancer, Anti-Aging, Anti-Melanogenesis, Detoxification, and Drug Delivery

by Arzu Zeynep Karabay, Jaleh Barar, Yalda Hekmatshoar and Yalda Rahbar Saadat

Biomolecules 2025, 15(3), 394; https://doi.org/10.3390/biom15030394 - 10 Mar 2025

Abstract

Most eukaryotic and prokaryotic cells have the potential to secrete a group of structures/membrane-bound organelles, collectively referred to as extracellular vesicles (EVs), which offer several advantages to producer/receiver cells. This review provides an overview of EVs from plant sources with emphasis on their [...] Read more.

Most eukaryotic and prokaryotic cells have the potential to secrete a group of structures/membrane-bound organelles, collectively referred to as extracellular vesicles (EVs), which offer several advantages to producer/receiver cells. This review provides an overview of EVs from plant sources with emphasis on their health-promoting potential and possible use as therapeutic agents. This review highlights the essential biological effects of plant-derived extracellular vesicles, including immune modulation, anticancer activities, protection against chemical toxicity and pathogens, as well as anti-aging, anti-melanogenesis, and anti-arthritic effects, along with ongoing clinical studies. Evidence revealed that plant-derived EVs’ contents exert their beneficial properties through regulating important signaling pathways by transferring miRNAs and other components. Taken all together, the data proposed that plant-derived EVs can be utilized as nutritional compounds and therapeutic agents, such as drug carriers. However, this emerging research area requires further in vitro/in vivo studies and clinical trials to determine the exact underlying mechanisms of EVs’ positive health effects in treating various diseases. Full article

(This article belongs to the Section Biological Factors)

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15 pages, 1874 KiB

Open AccessArticle

Genetic Analysis and Predictive Modeling of COVID-19 Severity in a Hospital-Based Patient Cohort

by Iraide Alloza-Moral, Ane Aldekoa-Etxabe, Raquel Tulloch-Navarro, Ainhoa Fiat-Arriola, Carmen Mar, Eloisa Urrechaga, Cristina Ponga, Isabel Artiga-Folch, Naiara Garcia-Bediaga, Patricia Aspichueta, Cesar Martin, Aitor Zarandona-Garai, Silvia Pérez-Fernández, Eunate Arana-Arri, Juan-Carlos Triviño, Ane Uranga, Pedro-Pablo España and Koen Vandenbroeck-van-Caeckenbergh

Biomolecules 2025, 15(3), 393; https://doi.org/10.3390/biom15030393 - 10 Mar 2025

Abstract

The COVID-19 pandemic has had a devastating impact, with more than 7 million deaths worldwide. Advanced age and comorbidities partially explain severe cases of the disease, but genetic factors also play a significant role. Genome-wide association studies (GWASs) have been instrumental in identifying [...] Read more.

The COVID-19 pandemic has had a devastating impact, with more than 7 million deaths worldwide. Advanced age and comorbidities partially explain severe cases of the disease, but genetic factors also play a significant role. Genome-wide association studies (GWASs) have been instrumental in identifying loci associated with SARS-CoV-2 infection. Here, we report the results from a >820 K variant GWAS in a COVID-19 patient cohort from the hospitals associated with IIS Biobizkaia. We compared intensive care unit (ICU)-hospitalized patients with non-ICU-hospitalized patients. The GWAS was complemented with an integrated phenotype and genetic modeling analysis using HLA genotypes, a previously identified COVID-19 polygenic risk score (PRS) and clinical data. We identified four variants associated with COVID-19 severity with genome-wide significance (rs58027632 in KIF19; rs736962 in HTRA1; rs77927946 in DMBT1; and rs115020813 in LINC01283). In addition, we designed a multivariate predictive model including HLA, PRS and clinical data which displayed an area under the curve (AUC) value of 0.79. Our results combining human genetic information with clinical data may help to improve risk assessment for the development of a severe outcome of COVID-19. Full article

(This article belongs to the Special Issue Metabolic Pathways, COVID-19 and Other Viral Acute Respiratory Infections: Mechanisms and Clinical Implications: 2nd Edition)

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28 pages, 2768 KiB

Open AccessReview

Pleiotropic Effects of Grm7/GRM7 in Shaping Neurodevelopmental Pathways and the Neural Substrate of Complex Behaviors and Disorders

by Beatrix M. Gyetvai and Csaba Vadasz

Biomolecules 2025, 15(3), 392; https://doi.org/10.3390/biom15030392 - 8 Mar 2025

Abstract

Natural gene variants of metabotropic glutamate receptor subtype 7 (Grm7), coding for mGluR7, affect individuals’ alcohol-drinking preference. Psychopharmacological investigations have suggested that mGluR7 is also involved in responses to cocaine, morphine, and nicotine exposures. We review the pleiotropic effects of Grm7 [...] Read more.

Natural gene variants of metabotropic glutamate receptor subtype 7 (Grm7), coding for mGluR7, affect individuals’ alcohol-drinking preference. Psychopharmacological investigations have suggested that mGluR7 is also involved in responses to cocaine, morphine, and nicotine exposures. We review the pleiotropic effects of Grm7 and the principle of recombinant quantitative trait locus introgression (RQI), which led to the discovery of the first mammalian quantitative gene accounting for alcohol-drinking preference. Grm7/GRM7 can play important roles in mammalian ontogenesis, brain development, and predisposition to addiction. It is also involved in other behavioral phenotypes, including emotion, stress, motivated cognition, defensive behavior, and pain-related symptoms. This review identified pleiotropy and the modulation of neurobehavioral processes by variations in the gene Grm7/GRM7. Patterns of pleiotropic genes can form oligogenic architectures whosecombined additive and interaction effects can significantly predispose individuals to the expressions of disorders. Identifying and characterizing pleiotropic genes are necessary for understanding the expressions of complex traits. This requires tasks, such as discovering and identifying novel genetic elements of the genetic architecture, which are unsuitable for AI but require classical experimental genetics. Full article

(This article belongs to the Special Issue Glutamate and Glutamate Receptors in Health and Diseases, Second Edition)

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15 pages, 4487 KiB

Open AccessArticle

Evaluation of Lipid-Based Transfection in Primary Monocytes Within an Ex Vivo Whole-Blood Model

by Robin Moolan-Vadackumchery, Lan Zhang and Frank Stüber

Biomolecules 2025, 15(3), 391; https://doi.org/10.3390/biom15030391 - 8 Mar 2025

Abstract

Transfection is a fundamental method in biomedical research to study intracellular molecular mechanisms by manipulating target protein expression. Various methods have been developed to deliver nucleic acids into the cells of interest in vitro, with chemical transfection by cationic lipids being the [...] Read more.

Transfection is a fundamental method in biomedical research to study intracellular molecular mechanisms by manipulating target protein expression. Various methods have been developed to deliver nucleic acids into the cells of interest in vitro, with chemical transfection by cationic lipids being the most widely used for RNA interference (RNAi). However, translating these in vitro results into in vivo remains a significant challenge. In this study, we established an ex vivo transfection model using cationic lipids in human whole blood. Three different lipid-based reagents were evaluated regarding toxicity, transfection efficiency, and immunogenicity across leukocyte populations using spectral flow cytometry. CD14⁺ monocytes were identified as the primary population to be transfected by cationic lipids in whole blood. To assess immunogenicity, the monocyte-specific activation markers CD80 and human leukocyte antigen DR isotype (HLA-DR) were analyzed upon transfection. Our results demonstrated that Lipofectamine RNAiMAX outperforms the other two reagents, showing low toxicity and high transfection efficiency in combination with a minimal potential for monocyte activation. Functional knockdown experiments using siRNA targeting CIITA and the microRNA mir-3972 targeting HLA-DRA showed dose-dependent suppression in HLA-DR expression. This study provides the framework for preliminary testing of RNAi in a physiologically relevant ex vivo model, enabling assessment of key endpoints such as toxicity, transfection efficiency, and immune activation potential of gene delivery systems. Full article

(This article belongs to the Section Cellular Biochemistry)

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20 pages, 1894 KiB

Open AccessArticle

Phytohormone and Amino Acid Changes in Cherry Radish as Metabolic Adaptive Response to Arsenic Single and Multi-Contamination

by Daniela Pavlíková, Veronika Zemanová, Milan Pavlík, Marie Lhotská, Jan Kubeš, Milan Novák, Petre I. Dobrev and Václav Motyka

Biomolecules 2025, 15(3), 390; https://doi.org/10.3390/biom15030390 - 8 Mar 2025

Abstract

This study investigated the metabolic adaptive responses to As contamination and As co-contamination with cadmium, lead, and zinc in the leaves and tubers of cherry radish (Raphanus sativus var. sativus Pers.). The response was assessed by measuring malondialdehyde levels, total phenolic content [...] Read more.

This study investigated the metabolic adaptive responses to As contamination and As co-contamination with cadmium, lead, and zinc in the leaves and tubers of cherry radish (Raphanus sativus var. sativus Pers.). The response was assessed by measuring malondialdehyde levels, total phenolic content (TPC), total anthocyanin pigment (TAC), growth and stress phytohormone concentration, and free amino acid content. The characteristic As accumulation of single contamination resulted in a decrease in tuber growth. However, in the case of co-contamination, As uptake was influenced by the presence of other potentially toxic elements (PTEs), mainly zinc, with no significant effect on growth. Both contaminated treatments exhibited significant differences in metabolite levels among the organs, along with notable changes in their contents. Increases in malondialdehyde, TPC, and TAC indicated induced oxidative stress and an antioxidant response that was more pronounced by As co-contamination. Also, the results for phytohormones, which showed both increases and decreases, along with selected free amino acids (which showed increases), demonstrated a more significant influence of As co-contamination. Based on these findings, it can be concluded that the response of cherry radish to contaminated treatments exhibited significant differences in the studied parameters, along with variability in the results, reflecting the extent of the effects of PTEs that induce oxidative stress. Full article

(This article belongs to the Section Natural and Bio-derived Molecules)

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18 pages, 4051 KiB

Open AccessArticle

Effects of Brimonidine, Latanoprost, and Omidenepag on Tunicamycin-Induced Endoplasmic Reticulum Stress and Fibrosis in Human Trabecular Meshwork Cells

by Mengxuan Liu, Megumi Honjo, Reiko Yamagishi and Makoto Aihara

Biomolecules 2025, 15(3), 389; https://doi.org/10.3390/biom15030389 - 8 Mar 2025

Abstract

This study evaluated the effects of α2-adrenergic agonist, prostaglandin F2α analog, and EP2 receptor agonist on tunicamycin-induced endoplasmic reticulum (ER) stress and fibrosis in human trabecular meshwork (TM) cells. Human TM cells were treated with tunicamycin for 24 h, followed by cotreatment with [...] Read more.

This study evaluated the effects of α2-adrenergic agonist, prostaglandin F2α analog, and EP2 receptor agonist on tunicamycin-induced endoplasmic reticulum (ER) stress and fibrosis in human trabecular meshwork (TM) cells. Human TM cells were treated with tunicamycin for 24 h, followed by cotreatment with brimonidine (BRI), latanoprost (LAT), or omidenepag (OMD). Immunocytochemistry was used to assess expressions of collagen type I alpha 1 chain (COL1A1), fibronectin, F-actin, and alpha-smooth muscle actin (α-SMA). Western blotting was performed to evaluate levels of C/EBP homologous protein (CHOP), 78-kDa glucose-regulated protein (GRP78), and splicing X-box binding protein-1 (sXBP-1). Real-time qPCR was used to examine the mRNA expressions of COL1A1, connective tissue growth factor (CTGF), fibronectin, α-SMA, CHOP, GRP78, and sXBP-1. Expressions of COL1A1, CTGF, F-actin, fibronectin, α-SMA, CHOP, GRP78, and sXBP-1 significantly increased after tunicamycin treatment. BRI cotreatment significantly downregulated the mRNA and protein expressions of GRP78, and LAT or OMD cotreatment significantly reduced the CHOP and sXBP-1 expressions compared to the tunicamycin-treated group. BRI, LAT, or OMD cotreatment significantly attenuated cellular cytoskeletal changes and the increase of fibrosis markers such as COL1A1, CTGF, fibronectin, and α-SMA. In addition, COL1A1 mRNA expression was significantly lowered with LAT or OMD cotreatment compared to the BRI-cotreated group. Cotreatment with α2-adrenergic agonist, prostaglandin F2α analog, or EP2 receptor agonist alleviates tunicamycin-induced ER stress in human TM cells. Full article

(This article belongs to the Section Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates)

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23 pages, 1077 KiB

Open AccessReview

Intestinal-Failure-Associated Liver Disease: Beyond Parenteral Nutrition

by Irene Mignini, Giulia Piccirilli, Federica Di Vincenzo, Carlo Covello, Marco Pizzoferrato, Giorgio Esposto, Linda Galasso, Raffaele Borriello, Maurizio Gabrielli, Maria Elena Ainora, Antonio Gasbarrini and Maria Assunta Zocco

Biomolecules 2025, 15(3), 388; https://doi.org/10.3390/biom15030388 - 8 Mar 2025

Abstract

Short bowel syndrome (SBS), usually resulting from massive small bowel resections or congenital defects, may lead to intestinal failure (IF), requiring intravenous fluids and parenteral nutrition to preserve patients’ nutritional status. Approximately 15% to 40% of subjects with SBS and IF develop chronic [...] Read more.

Short bowel syndrome (SBS), usually resulting from massive small bowel resections or congenital defects, may lead to intestinal failure (IF), requiring intravenous fluids and parenteral nutrition to preserve patients’ nutritional status. Approximately 15% to 40% of subjects with SBS and IF develop chronic hepatic damage during their life, a condition referred to as intestinal-failure-associated liver disease (IFALD), which ranges from steatosis to fibrosis or end-stage liver disease. Parenteral nutrition has been largely pointed out as the main pathogenetic factor for IFALD. However, other elements, such as inflammation, bile acid metabolism, bacterial overgrowth and gut dysbiosis also contribute to the development of liver damage and may deserve specific treatment strategies. Indeed, in our review, we aim to explore IFALD pathogenesis beyond parenteral nutrition. By critically analyzing recent literature, we seek to delve with molecular mechanisms and metabolic pathways underlying liver damage in such a complex set of patients. Full article

(This article belongs to the Special Issue Liver Damage and Associated Metabolic Disorders)

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17 pages, 2313 KiB

Open AccessArticle

Prognostic and Therapeutic Implications of Alamandine Receptor MrgD Expression in Clear Cell Renal Cell Carcinoma with Development of Metastatic Disease

by Gorka Larrinaga, Jon Danel Solano-Iturri, Inés Arrieta-Aguirre, Asier Valdivia, David Lecumberri, Ane Miren Iturregui, Charles H. Lawrie, María Armesto, Juan F. Dorado, Caroline E. Nunes-Xavier, Rafael Pulido, José I. López and Javier C. Angulo

Biomolecules 2025, 15(3), 387; https://doi.org/10.3390/biom15030387 - 7 Mar 2025

Abstract

Despite advances in the management of advanced clear cell renal cell carcinoma (ccRCC), robust biomarkers for prognosis and therapeutic response prediction remain elusive. Dysregulation of the intrarenal renin–angiotensin system (RAS) has been implicated in renal carcinogenesis but little explored, particularly regarding biomarker discovery [...] Read more.

Despite advances in the management of advanced clear cell renal cell carcinoma (ccRCC), robust biomarkers for prognosis and therapeutic response prediction remain elusive. Dysregulation of the intrarenal renin–angiotensin system (RAS) has been implicated in renal carcinogenesis but little explored, particularly regarding biomarker discovery and therapeutic innovation. Consequently, this study investigates the immunohistochemical expression and clinical relevance of the Mas-related G-protein-coupled receptor D (MrgD) in patients with ccRCC who developed metastatic disease (mccRCC). A cohort of 132 patients treated between 2008 and 2018 with nephrectomy and tyrosine kinase inhibitor (TKI)-based sequential therapy was analyzed. Treatment response was assessed using both the MASS and RECIST scoring systems. High MrgD expression in primary tumors was significantly associated with larger size, advanced stage, higher histological grade, and worse overall survival. Among 81 patients with metachronous metastases, high MrgD expression independently predicted shorter disease-free survival. High MrgD staining intensity correlated with poorer TKI responses in first-line therapy but improved outcomes with second-line mTORC1 inhibitors. These findings suggest that MrgD may be a useful biomarker of RAS linked to tumor aggressiveness in ccRCC. MrgD holds potential for identifying high-risk patients and guiding treatment selection in advanced disease. Further research is needed to unlock its clinical potential. Full article

(This article belongs to the Special Issue New Insights into Kidney Disease Development and Therapy Strategies)

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15 pages, 33993 KiB

Open AccessArticle

Immunohistochemical Detection of PIEZO Ion Channels in the Human Carotid Sinus and Carotid Body

by Elda Alba, Yolanda García-Mesa, Ramón Cobo, Patricia Cuendias, José Martín-Cruces, Iván Suazo, Graciela Martínez-Barbero, José A. Vega, Olivia García-Suárez and Teresa Cobo

Biomolecules 2025, 15(3), 386; https://doi.org/10.3390/biom15030386 - 7 Mar 2025

Abstract

The carotid sinus and the carotid body are major peripheral chemo- and baro(mechano)receptors that sense changes in arterial wall pressure and in oxygen, carbon dioxide, and pH in arterial blood. Recently, it was demonstrated that the PIEZO1 and PIEZO2 mechanoreceptor/mechanotransducers are responsible for [...] Read more.

The carotid sinus and the carotid body are major peripheral chemo- and baro(mechano)receptors that sense changes in arterial wall pressure and in oxygen, carbon dioxide, and pH in arterial blood. Recently, it was demonstrated that the PIEZO1 and PIEZO2 mechanoreceptor/mechanotransducers are responsible for the baroreflex in the murine aortic arch (aortic sinus). Furthermore, some experimental evidence suggests that the carotid body could participate in mechanosensing. In this study, we used immunohistochemistry and immunofluorescence in conjunction with laser confocal microscopy to study the distribution of PIEZO1 and PIEZO2 in the human carotid sinus and carotid body as well as in the petrosal ganglion of the glossopharyngeal nerve and the superior cervical sympathetic ganglion. PIEZO1 and PIEZO2 were detected in different morphotypes of sensory nerve formations in the walls of the carotid sinus and carotid artery walls. In the carotid body, PIEZO1 was present in a small population of type I glomus cells and absent in nerves, whereas PIEZO2 was present in both clusters of type I glomus cells and nerves. The most prominent expression of PIEZO1 and PIEZO2 in the carotid body was found in type II glomus cells. On the other hand, in the petrosal ganglion, around 25% of neurons were PIEZO1-positive, and around 85% were PIEZO2-positive; regarding the superior cervical sympathetic ganglion, around 71% and 86% displayed PIEZO1 and PIEZO2, respectively. The results of this study suggest that PIEZO1 and PIEZO2 could be involved in the detection and/or mechanotransduction of the human carotid sinus, whereas the role of the carotid body is more doubtful since PIEZO1 and PIEZO2 were only detected in some nerves and PIEZO2 was present in a small population of type I glomus cells, with PIEZO1 being absent in these cells. However, since immunoreactivity for PIEZO2 was detected in type II glomus cells, researchers should investigate whether these cells play a role in the detection of mechanical stimuli and/or participate in mechanotransduction. Full article

(This article belongs to the Section Molecular Biology)

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21 pages, 3711 KiB

Open AccessArticle

Metabolomic Profiling and In Vitro Evaluation of Cytotoxic, Genotoxic, and Antigenotoxic Effects of Staphylea pinnata L. Extract from Italian Flora

by Ghanya Al-Naqeb, Fabio Pietrolucci, Mauro Commisso, Aliki Kalmpourtzidou, Amanda Oldani, Sara Boussetta, Beatrice Maccarini, Rachele De Giuseppe and Hellas Cena

Biomolecules 2025, 15(3), 385; https://doi.org/10.3390/biom15030385 - 6 Mar 2025

Abstract

Staphylea pinnata L., (S. pinnata), has long been recognized in Europe as both a wild food source and a traditional medicinal. This study aimed to characterize the metabolomic profile of the leaf extract of S. pinnata and assess its cytotoxic, genotoxic, [...] Read more.

Staphylea pinnata L., (S. pinnata), has long been recognized in Europe as both a wild food source and a traditional medicinal. This study aimed to characterize the metabolomic profile of the leaf extract of S. pinnata and assess its cytotoxic, genotoxic, and antigenotoxic effects in vitro for the first time. The methanolic extract of the leaves was analyzed using Ultra-Performance Liquid Chromatography–High-Resolution Mass Spectrometry (UPLC-HRMS). To evaluate its cytotoxic, genotoxic, and antigenotoxic properties, the cytokinesis block micronucleus assay was performed on Chinese hamster ovarian K1 cells. The analysis revealed a wide variety of metabolites in the extract, with B-type procyanidins and prodelphinidins being the most abundant. The genotoxicity of the extract varied depending on its concentration; at the lowest concentration (75 μg/mL), it showed no genotoxic effects and exhibited antigenotoxic properties by reducing the frequency of micronuclei induced by mitomycin C. However, at the highest concentration (300 μg/mL), the extract demonstrated genotoxic effects. In conclusion, the S. pinnata extract displayed both genotoxic and antigenotoxic properties, which may be attributed to its phytochemical composition. These findings highlight the complex nature of the plant’s bioactive compounds, suggesting potential therapeutic applications with careful consideration of dosage. Additional research is necessary to understand the mechanisms underlying these properties. Full article

(This article belongs to the Special Issue Natural Bioactives as Leading Molecules for Drug Development)

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11 pages, 340 KiB

Open AccessReview

Current and Emerging Assays for Measuring Human T-Cell Responses Against Beta-Cell Antigens in Type 1 Diabetes

by Ting-Chen Lin, Matthew Lacorcia and Stuart I. Mannering

Biomolecules 2025, 15(3), 384; https://doi.org/10.3390/biom15030384 - 6 Mar 2025

Abstract

Type 1 diabetes (T1D) is an autoimmune disease caused by T-cell mediated destruction of the pancreatic insulin-producing beta cells. Currently, the development of autoantibodies is the only measure of beta-cell autoimmunity used in the clinic. Despite T-cells’ well-accepted role in the autoimmune pathogenesis [...] Read more.

Type 1 diabetes (T1D) is an autoimmune disease caused by T-cell mediated destruction of the pancreatic insulin-producing beta cells. Currently, the development of autoantibodies is the only measure of beta-cell autoimmunity used in the clinic. Despite T-cells’ well-accepted role in the autoimmune pathogenesis of human T1D, autoimmune T-cell responses against beta cells remain very difficult to measure. An assay capable of measuring beta-cell antigen-specific T-cell responses has been a long-sought goal. Such an assay would facilitate the direct monitoring of T1D-associated T-cell responses facilitating, earlier diagnosis and rapid evaluation of candidate immune therapies in clinical trials. In addition, a simple and robust assay for beta-cell antigen-specific T-cell responses would be a powerful tool for dissecting the autoimmune pathogenesis of human T1D. Here, we review the challenges associated with measuring beta-cell antigen-specific T-cell responses, the current assays which are used to achieve this and, finally, we discuss BASTA, a promising emerging assay for measuring human beta-cell antigen-specific CD4⁺ T-cell responses. Full article

(This article belongs to the Special Issue Immune Responses in Type 1 Diabetes)

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20 pages, 746 KiB

Open AccessReview

The Association Among Bipolar Disorder, Mitochondrial Dysfunction, and Reactive Oxygen Species

by Yuki Kageyama, Shohei Okura, Ayaka Sukigara, Ayaka Matsunaga, Kunio Maekubo, Takafumi Oue, Koki Ishihara, Yasuhiko Deguchi and Koki Inoue

Biomolecules 2025, 15(3), 383; https://doi.org/10.3390/biom15030383 - 6 Mar 2025

Abstract

Mitochondria, often known as the cell’s powerhouses, are primarily responsible for generating energy through aerobic oxidative phosphorylation. However, their functions extend far beyond just energy production. Mitochondria play crucial roles in maintaining calcium balance, regulating apoptosis (programmed cell death), supporting cellular signaling, influencing [...] Read more.

Mitochondria, often known as the cell’s powerhouses, are primarily responsible for generating energy through aerobic oxidative phosphorylation. However, their functions extend far beyond just energy production. Mitochondria play crucial roles in maintaining calcium balance, regulating apoptosis (programmed cell death), supporting cellular signaling, influencing cell metabolism, and synthesizing reactive oxygen species (ROS). Recent research has highlighted a strong link between bipolar disorder (BD) and mitochondrial dysfunction. Mitochondrial dysfunction contributes to oxidative stress, particularly through the generation of ROS, which are implicated in the pathophysiology of BD. Oxidative stress arises when there is an imbalance between the production of ROS and the cell’s ability to neutralize them. In neurons, excessive ROS can damage various cellular components, including proteins in neuronal membranes and intracellular enzymes. Such damage may interfere with neurotransmitter reuptake and the function of critical enzymes, potentially affecting brain regions involved in mood regulation and emotional control, which are key aspects of BD. In this review, we will explore how various types of mitochondrial dysfunction contribute to the production of ROS. These include disruptions in energy metabolism, impaired ROS management, and defects in mitochondrial quality control mechanisms such as mitophagy (the process by which damaged mitochondria are selectively degraded). We will also examine how abnormalities in calcium signaling, which is crucial for synaptic plasticity, can lead to mitochondrial dysfunction. Additionally, we will discuss the specific mitochondrial dysfunctions observed in BD, highlighting how these defects may contribute to the disorder’s pathophysiology. Finally, we will identify potential therapeutic targets to improve mitochondrial function, which could pave the way for new treatments to manage or mitigate symptoms of BD. Full article

(This article belongs to the Special Issue Mitochondrial ROS in Health and Disease)

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13 pages, 1868 KiB

Open AccessArticle

Efficient Incorporation of DOPA into Proteins Free from Competition with Endogenous Translation Termination Machinery

by Youhui Yang, Yingchen Wang, Zhaoguan Wang and Hao Qi

Biomolecules 2025, 15(3), 382; https://doi.org/10.3390/biom15030382 - 6 Mar 2025

Abstract

3,4-Dihydroxy-L-phenylalanine (DOPA) is a promising noncanonical amino acid (ncAA) that introduces novel catechol chemical features into proteins, expanding their functional potential. However, the most common approach to incorporating ncAAs into proteins relies on stop codon suppression, which is often limited by the competition [...] Read more.

3,4-Dihydroxy-L-phenylalanine (DOPA) is a promising noncanonical amino acid (ncAA) that introduces novel catechol chemical features into proteins, expanding their functional potential. However, the most common approach to incorporating ncAAs into proteins relies on stop codon suppression, which is often limited by the competition of endogenous translational termination machinery. Here, we employed a special in vitro protein expression system that facilitates the efficiency of DOPA incorporation into proteins by removing essential Class I peptide release factors through targeted degradation. In the absence of both RF1 and RF2, we successfully demonstrated DOPA incorporation at all three stop codons (TAG, TAA, and TGA). By optimizing the concentration of engineered DOPA-specific aminoacyl-tRNA synthetase (DOPARS), DOPA, and DNA template, we achieved a synthesis yield of 2.24 µg of sfGFP with 100% DOPA incorporation in a 20 μL reaction system. DOPARS exhibited a dissociation constant (Kd) of 11.7 μM for DOPA but showed no detectable binding to its native counterpart, tyrosine. Additionally, DOPA was successfully incorporated into a reverse transcriptase, which interfered with its activity. This system demonstrates a fast and efficient approach for precise DOPA incorporation into proteins, paving the way for advanced protein engineering applications. Full article

(This article belongs to the Special Issue Cutting-Edge Perspectives on Protein and Enzyme Engineering)

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22 pages, 6749 KiB

Open AccessArticle

Neurocellular Stress Response to Mojave Type A Rattlesnake Venom: Study of Molecular Mechanisms Using Human iPSC-Derived Neural Stem Cell Model

by Satish Kumar, Miriam Aceves, Jose Granados, Lorena Guerra, Felicia Juarez, Earl Novilla, Ana C. Leandro, Marcelo Leandro, Juan Peralta, Sarah Williams-Blangero, Elda E. Sanchez, Jacob A. Galan, John Blangero and Joanne E. Curran

Biomolecules 2025, 15(3), 381; https://doi.org/10.3390/biom15030381 - 6 Mar 2025

Abstract

The Mojave rattlesnake venom shows significant geographical variability. The venom of Type A animals primarily contains β-neurotoxin referred to as Mojave Toxin (MTX), which makes bites from this snake particularly feared. We performed a genome-wide transcriptomic analysis of the neurocellular response to Mojave [...] Read more.

The Mojave rattlesnake venom shows significant geographical variability. The venom of Type A animals primarily contains β-neurotoxin referred to as Mojave Toxin (MTX), which makes bites from this snake particularly feared. We performed a genome-wide transcriptomic analysis of the neurocellular response to Mojave Type A rattlesnake venom using induced pluripotent stem cell-derived neural stem cells to unveil the molecular mechanisms underlying the damage caused by this snake’s envenomation. Our results suggest that snake venom metalloproteases, although having a limited repertoire in Type A venom, facilitate venom spread by digesting the tissue’s extracellular matrix. The MTX, which is composed of heterodimers of basic and acidic phospholipase-A2, co-opts the host arachidonic acid and Ca²⁺ second messenger mechanisms and triggers multiple signaling cascades, such as the activation of MAPKs and NF-κB-regulated proinflammatory genes; the neurotransmitter overload in excitatory synapses leading to a presynaptic blockade of nerve signals; and the upregulation of unfolded protein response (UPR) due to the depletion of Ca²⁺ from the endoplasmic reticulum. The upregulated UPR and the oxidative stress caused by reactive oxygen species generated in cytochromeP4501A1-mediated hydroxylation of arachidonic acid contribute to mitochondrial toxicity. The activation of UPR, mitochondrial toxicity, and oxidative stress synergistically contributed to apoptotic and ferroptotic cell death. Full article

(This article belongs to the Special Issue Pluripotent Stem Cell Models of Human Disease)

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33 pages, 1933 KiB

Open AccessReview

Interplay Between Traditional and Scientific Knowledge: Phytoconstituents and Their Roles in Lung and Colorectal Cancer Signaling Pathways

by Ilma Imtiaz, Janet Schloss and Andrea Bugarcic

Biomolecules 2025, 15(3), 380; https://doi.org/10.3390/biom15030380 - 5 Mar 2025

Abstract

Natural plant products have been used for cancer treatment since ancient times and continue to play a vital role in modern anticancer drug development. However, only a small fraction of identified medicinal plants has been thoroughly investigated, particularly for their effects on cellular [...] Read more.

Natural plant products have been used for cancer treatment since ancient times and continue to play a vital role in modern anticancer drug development. However, only a small fraction of identified medicinal plants has been thoroughly investigated, particularly for their effects on cellular pathways in lung and colorectal cancers, two under-researched cancers with poor prognostic outcomes (lung cancers). This review focuses on the lung and colorectal cancer signaling pathways modulated by bioactive compounds from eleven traditional medicinal plants: Curcuma longa, Astragalus membranaceus, Glycyrrhiza glabra, Althaea officinalis, Echinacea purpurea, Sanguinaria canadensis, Codonopsis pilosula, Hydrastis canadensis, Lobelia inflata, Scutellaria baicalensis, and Zingiber officinale. These plants were selected based on their documented use in traditional medicine and modern clinical practice. Selection criteria involved cross-referencing herbs identified in a scoping review of traditional cancer treatments and findings from an international survey on herbal medicine currently used for lung and colorectal cancer management by our research group and the availability of existing literature on their anticancer properties. The review identifies several isolated phytoconstituents from these plants that exhibit anticancer properties by modulating key signaling pathways such as PI3K/Akt/mTOR, RAS/RAF/MAPK, Wnt/β-catenin, and TGF-β in vitro. Notable constituents include sanguinarine, berberine, hydrastine, lobeline, curcumin, gingerol, shogaol, caffeic acid, echinacoside, cichoric acid, glycyrrhizin, 18-β-glycyrrhetinic acid, astragaloside IV, lobetyolin, licochalcone A, baicalein, baicalin, wogonin, and glycyrol. Curcumin and baicalin show preclinical effectiveness but face bioavailability challenges, which may be overcome by combining them with piperine or using oral extracts to enhance gut microbiome conversion, integrating traditional knowledge with modern strategies for improved outcomes. Furthermore, herbal extracts from Echinacea, Glycyrrhiza, and Codonopsis, identified in traditional knowledge, are currently in clinical trials. Notably, curcumin and baicalin also modulate miRNA pathways, highlighting a promising intersection of modern science and traditional medicine. Thus, the development of anticancer therapeutics continues to benefit from the synergy of traditional knowledge, scientific innovation, and technological advancements. Full article

(This article belongs to the Special Issue Key Molecules in Traditional Medicine: From Molecular Mechanisms to Therapies Strategies)

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23 pages, 8998 KiB

Open AccessArticle

PRAG1 Condensation Drives Cell Contraction Under Stress

by Peiwu Ye, Peiran Jiang, Luyu Ye, Min Liu, Qiuyuan Fang, Peilin Yu, Jianhong Luo, Huanxing Su and Wei Yang

Biomolecules 2025, 15(3), 379; https://doi.org/10.3390/biom15030379 - 5 Mar 2025

Abstract

Peak1-related, kinase-activating pseudokinase 1 (PRAG1), a member of the pseudopodium-enriched atypical kinase (PEAK) family of pseudokinases, has been reported to play a role in regulating cell morphology. However, the molecular mechanism for this function remains elusive. In this study, we demonstrate that PRAG1 [...] Read more.

Peak1-related, kinase-activating pseudokinase 1 (PRAG1), a member of the pseudopodium-enriched atypical kinase (PEAK) family of pseudokinases, has been reported to play a role in regulating cell morphology. However, the molecular mechanism for this function remains elusive. In this study, we demonstrate that PRAG1 forms dynamic condensates in cells mediated by its αN and αJ helices. Importantly, we found that PRAG1 condensates functioned in mediating cell contraction, while condensate-formation-deficient PRAG1 mutants lost this function. Remarkably, the formation of spherical PRAG1 condensates appears to be a common phenomenon in diverse stress models, as well as in dopaminergic (DA) neurons derived from a Parkinson’s disease patient. Our findings reveal a novel mechanism through which PRAG1 drives cell contraction and suggest a potential link between aberrant PRAG1 phase separation and stress-induced cell contraction. PRAG1 condensation drives cell contraction under stress. Full article

(This article belongs to the Section Molecular Biology)

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28 pages, 1531 KiB

Open AccessReview

Deep Thought on the HIV Cured Cases: Where Have We Been and What Lies Ahead?

by Qing Xiao, Sanxiu He, Chaoyu Wang, Yixing Zhou, Chensi Zeng, Jun Liu, Tingting Liu, Tingting Li, Xi Quan, Linyue Wang, Liuyue Zhai, Yi Liu, Jun Li, Xiaomei Zhang and Yao Liu

Biomolecules 2025, 15(3), 378; https://doi.org/10.3390/biom15030378 - 5 Mar 2025

Abstract

Antiretroviral therapy (ART) can effectively suppress the replication of human immunodeficiency virus (HIV), but it cannot completely eradicate the virus. The persistent existence of the HIV reservoir is a major obstacle in the quest for a cure. To date, there have been a [...] Read more.

Antiretroviral therapy (ART) can effectively suppress the replication of human immunodeficiency virus (HIV), but it cannot completely eradicate the virus. The persistent existence of the HIV reservoir is a major obstacle in the quest for a cure. To date, there have been a total of seven cured cases of HIV worldwide. These patients all cleared HIV while undergoing allogeneic stem cell transplantation (allo-HSCT) for hematological malignancies. However, in these cases, the specific mechanism by which allo-HSCT leads to the eradication of HIV remains unclear, so it is necessary to conduct an in-depth analysis. Due to the difficulty in obtaining donors and the risks associated with transplantation, this treatment method is not applicable to all HIV patients. There is still a need to explore new treatment strategies. In recent years, emerging therapies such as neutralizing antibody immunotherapy, chimeric antigen receptor T cell (CAR-T) therapy, gene editing, and antiviral therapies targeting the reservoir have attracted wide attention due to their ability to effectively inhibit HIV replication. This article first elaborates on the nature of the HIV reservoir, then deeply explores the treatment modalities and potential success factors of HIV cured cases, and finally discusses the current novel treatment methods, hoping to provide comprehensive and feasible strategies for achieving the cure of HIV. Full article

(This article belongs to the Section Molecular Medicine)

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12 pages, 1759 KiB

Open AccessCommunication

Indoleacetylglutamine Pathway Is a Potential Biomarker for Cardiovascular Diseases

by Khaled Naja, Najeha Anwardeen, Mashael Al-Shafai and Mohamed A. Elrayess

Biomolecules 2025, 15(3), 377; https://doi.org/10.3390/biom15030377 - 5 Mar 2025

Abstract

Cardiovascular diseases (CVDs) remain a leading cause of global morbidity and mortality. Metabolomics allows for the identification of important biomarkers for CVDs, essential for early detection and risk assessment. This cross-sectional study aimed to identify novel metabolic biomarkers associated with CVDs using non-targeted [...] Read more.

Cardiovascular diseases (CVDs) remain a leading cause of global morbidity and mortality. Metabolomics allows for the identification of important biomarkers for CVDs, essential for early detection and risk assessment. This cross-sectional study aimed to identify novel metabolic biomarkers associated with CVDs using non-targeted metabolomics. We compared the metabolic profiles of 112 patients with confirmed CVDs diagnosis and 112 gender- and age-matched healthy controls from the Qatar Biobank database. Orthogonal partial least square discriminate analysis and linear models were used to analyze differences in the level of metabolites between the two groups. We report here a significant association between the indoleacetylglutamine pathway and cardiovascular diseases, expanding the repertoire of gut microbiota metabolites linked to CVDs. Our findings suggest that alterations in gut microbiota metabolism, potentially resulting in increased production of indoleacetate, indoleacetylglutamine, and related compounds at the expense of the cardioprotective indolepropionate, may contribute to this association. Our findings may pave the way for novel approaches in CVD risk assessment and potential therapeutic interventions targeting the gut-heart axis. Full article

(This article belongs to the Special Issue Biomarkers of Cardiovascular and Cerebrovascular Diseases, 2nd Edition)

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30 pages, 6713 KiB

Open AccessReview

The Progress and Evolving Trends in Nucleic-Acid-Based Therapies

by Yunlong Liu, Chunmiao Wang, Xiuping Fu and Mengtian Ren

Biomolecules 2025, 15(3), 376; https://doi.org/10.3390/biom15030376 - 5 Mar 2025

Abstract

Nucleic-acid-based therapies have emerged as a pivotal domain within contemporary biomedical science, marked by significant advancements in recent years. These innovative treatments primarily operate through the precise binding of DNA or RNA molecules to discrete target genes, subsequently suppressing the expression of the [...] Read more.

Nucleic-acid-based therapies have emerged as a pivotal domain within contemporary biomedical science, marked by significant advancements in recent years. These innovative treatments primarily operate through the precise binding of DNA or RNA molecules to discrete target genes, subsequently suppressing the expression of the target proteins. The spectrum of nucleic-acid-based therapies encompasses antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs), etc. Compared to more traditional medicinal approaches, nucleic-acid-based therapies stand out for their highly targeted action on specific genes, as well as their potential for chemical modification to improve resistance to nucleases, ensuring sustained therapeutic activity and mitigating immunogenicity concerns. Nevertheless, these molecules’ limited cellular permeability necessitates the deployment of delivery vectors to enhance their intracellular uptake and stability. As nucleic-acid-based therapies progressively display promising pharmacodynamic profiles, there has been a burgeoning interest in these treatments for applications in clinical research. This review aims to summarize the variety of nucleic acid drugs and their mechanisms, evaluate the present status in research and application, discourse on prospective trends, and potential challenges ahead. These innovative therapeutics are anticipated to assume a pivotal role in the management of a wide array of diseases. Full article

(This article belongs to the Section Biomacromolecules: Proteins, Nucleic Acids and Carbohydrates)

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