International Journal of Molecular Sciences

14 pages, 288 KiB

Open AccessReview

Immunotherapy and Cancer: The Multi-Omics Perspective

by Clelia Donisi, Andrea Pretta, Valeria Pusceddu, Pina Ziranu, Eleonora Lai, Marco Puzzoni, Stefano Mariani, Elena Massa, Clelia Madeddu and Mario Scartozzi

Int. J. Mol. Sci. 2024, 25(6), 3563; https://doi.org/10.3390/ijms25063563 - 21 Mar 2024

Cited by 2 | Viewed by 2293

Abstract

Immunotherapies have revolutionized cancer treatment approaches. Because not all patients respond positively to immune therapeutic agents, it represents a challenge for scientists who strive to understand the mechanisms behind such resistance. In-depth exploration of tumor biology, using novel technologies such as omics science, [...] Read more.

Immunotherapies have revolutionized cancer treatment approaches. Because not all patients respond positively to immune therapeutic agents, it represents a challenge for scientists who strive to understand the mechanisms behind such resistance. In-depth exploration of tumor biology, using novel technologies such as omics science, can help decode the role of the tumor immune microenvironment (TIME) in producing a response to the immune blockade strategies. It can also help to identify biomarkers for patient stratification and personalized treatment. This review aims to explore these new models and highlight their possible pivotal role in changing clinical practice. Full article

(This article belongs to the Special Issue State-of-the-Art Cancer Immunotherapies)

35 pages, 3878 KiB

Open AccessReview

Therapeutic Applications of Stem Cell-Derived Exosomes

by Omar Abdulhakeem Ahmed Yusuf Abdulmalek, Khaled Hameed Husain, Haya Khaled Ali Abdulla AlKhalifa, Mariam Masood Abdulkarim Bahrooz Alturani, Alexandra E. Butler and Abu Saleh Md Moin

Int. J. Mol. Sci. 2024, 25(6), 3562; https://doi.org/10.3390/ijms25063562 - 21 Mar 2024

Cited by 9 | Viewed by 4376

Abstract

Exosomes are extracellular vesicles of endosomal origin, ranging from 30 to 150 nm in diameter, that mediate intercellular transfer of various biomolecules, such as proteins, lipids, nucleic acids, and metabolites. They modulate the functions of recipient cells and participate in diverse physiological and [...] Read more.

Exosomes are extracellular vesicles of endosomal origin, ranging from 30 to 150 nm in diameter, that mediate intercellular transfer of various biomolecules, such as proteins, lipids, nucleic acids, and metabolites. They modulate the functions of recipient cells and participate in diverse physiological and pathological processes, such as immune responses, cell–cell communication, carcinogenesis, and viral infection. Stem cells (SCs) are pluripotent or multipotent cells that can differentiate into various cell types. SCs can also secrete exosomes, which exhibit remarkable therapeutic potential for various diseases, especially in the field of regenerative medicine. For example, exosomes derived from mesenchymal stem cells (MSCs) contain proteins, lipids, and miRNAs that can ameliorate endocrine disorders, such as diabetes and cancer. Exosomes from SCs (sc-exos) may offer similar advantages as SCs, but with reduced risks and challenges. Sc-exos have lower tumorigenicity, immunogenicity, and infectivity. They can also deliver drugs more efficiently and penetrate deeper into tissues. In this review, we provide an overview of the recent advances in sc-exos and their therapeutic applications in various diseases, such as diabetes and cancer. We also elucidate how the biological effects of sc-exos depend on their molecular composition. We also address the current challenges and future directions of using sc-exos. Full article

(This article belongs to the Special Issue Exosomes and Extracellular Vesicles in Health and Diseases 2.0)

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13 pages, 1403 KiB

Open AccessArticle

Tocotrienols Prevent the Decline of Learning Ability in High-Fat, High-Sucrose Diet-Fed C57BL/6 Mice

by Yugo Kato, Junhyoku Ben, Atsuto Noto, Shuntaro Kashiwaya, Yoshinori Aoki, Nobuo Watanabe, Hiroki Tsumoto, Yuri Miura and Koji Fukui

Int. J. Mol. Sci. 2024, 25(6), 3561; https://doi.org/10.3390/ijms25063561 - 21 Mar 2024

Viewed by 2502

Abstract

Obesity has been increasing worldwide and is well-known as a risk factor for cognitive decline. It has been reported that oxidative stress in the brain is deeply involved in cognitive dysfunction in rodent models. While there are many studies on oxidation in the [...] Read more.

Obesity has been increasing worldwide and is well-known as a risk factor for cognitive decline. It has been reported that oxidative stress in the brain is deeply involved in cognitive dysfunction in rodent models. While there are many studies on oxidation in the liver and adipose tissue of obese mice, the relationship between obesity-induced cognitive dysfunction and brain oxidation has not been elucidated. Here, we show that obesity induced by a high-fat, high-sucrose diet (HFSD) alters cognitive function in C57BL/6 male mice, and it may involve the acceleration of brain oxidation. Tocotrienols (T3s), which are members of the vitamin E family, can prevent HFSD-induced cognitive changes. To elucidate these mechanisms, respiratory metabolism, locomotor activity, temperature around brown adipose tissue, and protein profiles in the cerebrum cortex were measured. Contrary to our expectation, respiratory metabolism was decreased, and temperature around brown adipose tissue was increased in the feeding of HFSD. The proteins that regulate redox balance did not significantly change, but 12 proteins, which were changed by HFSD feeding and not changed by T3s-treated HFSD compared to control mice, were identified. Our results indicated that HFSD-induced obesity decreases mouse learning ability and that T3s prevent its change. Additionally, feeding of HFSD significantly increased brain oxidation. However, further study is needed to elucidate the mechanisms of change in oxidative stress in the brain by obesity. Full article

(This article belongs to the Special Issue Antioxidants in Health and Diseases)

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33 pages, 7079 KiB

Open AccessArticle

Extracellular Vesicle Protein Expression in Doped Bioactive Glasses: Further Insights Applying Anomaly Detection

by Mauro Nascimben, Hugo Abreu, Marcello Manfredi, Giuseppe Cappellano, Annalisa Chiocchetti and Lia Rimondini

Int. J. Mol. Sci. 2024, 25(6), 3560; https://doi.org/10.3390/ijms25063560 - 21 Mar 2024

Viewed by 1997

Abstract

Proteomic analysis of extracellular vesicles presents several challenges due to the unique nature of these small membrane-bound structures. Alternative analyses could reveal outcomes hidden from standard statistics to explore and develop potential new biological hypotheses that may have been overlooked during the initial [...] Read more.

Proteomic analysis of extracellular vesicles presents several challenges due to the unique nature of these small membrane-bound structures. Alternative analyses could reveal outcomes hidden from standard statistics to explore and develop potential new biological hypotheses that may have been overlooked during the initial evaluation of the data. An analysis sequence focusing on deviating protein expressions from donors’ primary cells was performed, leveraging machine-learning techniques to analyze small datasets, and it has been applied to evaluate extracellular vesicles’ protein content gathered from mesenchymal stem cells cultured on bioactive glass discs doped or not with metal ions. The goal was to provide additional opportunities for detecting details between experimental conditions that are not entirely revealed with classic statistical inference, offering further insights regarding the experimental design and assisting the researchers in interpreting the outcomes. The methodology extracted a set of EV-related proteins whose differences between conditions could be partially explainable with statistics, suggesting the presence of other factors involved in the bioactive glasses’ interactions with tissues. Outlier identification of extracellular vesicles’ protein expression levels related to biomaterial preparation was instrumental in improving the interpretation of the experimental outcomes. Full article

(This article belongs to the Special Issue Biomaterials for Dental and Orthopedic Applications)

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18 pages, 7017 KiB

Open AccessArticle

Expression of Placental Lipid Transporters in Pregnancies Complicated by Gestational and Type 1 Diabetes Mellitus

by Paweł Jan Stanirowski, Mateusz Wątroba, Michał Pyzlak, Jarosław Wejman and Dariusz Szukiewicz

Int. J. Mol. Sci. 2024, 25(6), 3559; https://doi.org/10.3390/ijms25063559 - 21 Mar 2024

Cited by 1 | Viewed by 1657

Abstract

The objective of the study was to assess the expression of proteins responsible for placental lipid transport in term pregnancies complicated by well-controlled gestational (GDM) and type 1 diabetes mellitus (PGDM). A total of 80 placental samples were obtained from patients diagnosed with [...] Read more.

The objective of the study was to assess the expression of proteins responsible for placental lipid transport in term pregnancies complicated by well-controlled gestational (GDM) and type 1 diabetes mellitus (PGDM). A total of 80 placental samples were obtained from patients diagnosed with PGDM (n = 20), GDM treated with diet (GDMG1, n = 20), GDM treated with diet and insulin (GDMG2, n = 20), and a non-diabetic control group (n = 20). Umbilical and uterine artery blood flows were assessed by means of ultrasound in the period prior to delivery and computer-assisted quantitative morphometry of immunostained placental sections was performed to determine the expression of selected proteins. The morphometric analysis performed for the vascular density-matched placental samples demonstrated a significant increase in the expression of fatty acid translocase (CD36), fatty acid binding proteins (FABP1, FABP4 and FABP5), as well as a decrease in the expression of endothelial lipase (EL) and fatty acid transport protein (FATP4) in the PGDM-complicated pregnancies as compared to the GDMG1 and control groups (p < 0.05). No significant differences with regard to the placental expression of lipoprotein lipase (LPL) and FATP6 protein between GDM/PGDM and non-diabetic patients were noted. Maternal pre-pregnancy weight, body mass index, placental weight as well as the expression of LPL and FABP4 were selected by the linear regression model as the strongest contributors to the fetal birth weight. To conclude, in placentas derived from pregnancies complicated by well-controlled PGDM, the expression of several lipid transporters, including EL, CD36, FATP4, FABP1, FABP4 and FABP5, is altered. Nonetheless, only LPL and FABP4 were significant predictors of the fetal birth weight. Full article

(This article belongs to the Special Issue Insights in Reproductive Immunology and Placental Pathology)

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23 pages, 5950 KiB

Open AccessArticle

Design, Synthesis, Anti-Inflammatory Activity, DFT Modeling and Docking Study of New Ibuprofen Derivatives

by Abbas M. Abbas, Hossam H. Nasrallah, Ahmed Aboelmagd, Safaa M. Kishk, W. Christopher Boyd, Haitham Kalil and Adel S. Orabi

Int. J. Mol. Sci. 2024, 25(6), 3558; https://doi.org/10.3390/ijms25063558 - 21 Mar 2024

Cited by 4 | Viewed by 1787

Abstract

A new ibuprofen derivative, (E)-2-(4-isobutylphenyl)-N′-(4-oxopentan-2-ylidene) propane hydrazide (IA), was synthesized, along with its metal complexes with Co, Cu, Ni, Gd, and Sm, to investigate their anti-inflammatory efficacy and COX-2 inhibition potential. Comprehensive characterization, including ¹H NMR, MS, FTIR, UV–vis spectroscopy, [...] Read more.

A new ibuprofen derivative, (E)-2-(4-isobutylphenyl)-N′-(4-oxopentan-2-ylidene) propane hydrazide (IA), was synthesized, along with its metal complexes with Co, Cu, Ni, Gd, and Sm, to investigate their anti-inflammatory efficacy and COX-2 inhibition potential. Comprehensive characterization, including ¹H NMR, MS, FTIR, UV–vis spectroscopy, and DFT analysis, were employed to determine the structural configurations, revealing unique motifs for Gd/Sm (capped square antiprismatic/tricapped trigonal prismatic) and Cu/Ni/Co (octahedral) complexes. Molecular docking with the COX-2 enzyme (PDB code: 5IKT) and pharmacokinetic assessments through SwissADME indicated that these compounds have superior binding energies and pharmacokinetic profiles, including BBB permeability and gastrointestinal absorption, compared to the traditional ibuprofen standalone. Their significantly lower IC50 values further suggest a higher efficacy as anti-inflammatory agents and COX-2 inhibitors. These research findings not only introduce promising ibuprofen derivatives for therapeutic applications but also set the stage for future validation and exploration of this new generation of ibuprofen compounds. Full article

(This article belongs to the Section Molecular Pharmacology)

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13 pages, 5281 KiB

Open AccessArticle

In Vitro Antibacterial Activity of Ozonated Olive Oil against Bacteria of Various Antimicrobial Resistance Profiles Isolated from Wounds of Companion Animals

by Anna Lenart-Boroń, Klaudia Stankiewicz, Klaudia Bulanda, Natalia Czernecka, Miłosz Heliasz, Walter Hunter, Anna Ratajewicz, Karen Khachatryan and Gohar Khachatryan

Int. J. Mol. Sci. 2024, 25(6), 3557; https://doi.org/10.3390/ijms25063557 - 21 Mar 2024

Cited by 1 | Viewed by 2127

Abstract

Frequent colonization and bacterial infection of skin wounds in small animals prevent or impair their healing. However, the broadly applied antimicrobial therapy of wounds is not always necessary and promotes the spread of bacterial resistance. Thus, alternatives to antimicrobial therapy, including preventive measures [...] Read more.

Frequent colonization and bacterial infection of skin wounds in small animals prevent or impair their healing. However, the broadly applied antimicrobial therapy of wounds is not always necessary and promotes the spread of bacterial resistance. Thus, alternatives to antimicrobial therapy, including preventive measures in the form of wound dressings with antibiotic properties, should be searched for. The aim of this study was to develop a new, efficient, cost-effective and non-toxic formulation with antimicrobial properties to serve as an alternative to antibiotic administration in wound-healing stimulation in companion animals. Nano/microencapsulated ozonated olive oil in a hyaluronan matrix was developed, with ozone concentration high enough to prevent bacterial growth. The presence and size of nano- and microcapsules were determined with scanning electron microscopy (SEM). Antibacterial activity of developed formulations was examined in vitro on 101 Gram-positive and Gram-negative bacteria isolated from the wounds of companion animals. The highest ozone concentration in the developed formulations inhibited the growth of 40.59% bacteria. Species and genus-specific differences in reactions were observed. Enterococcus spp. proved the least susceptible while non-pathogenic Gram-positive bacteria were the most susceptible to the examined formulations. Changes in the bacterial morphology and cell structure of Psychrobacter sanguinis suspension mixed with Ca-stabilized formulations with nano/microencapsulated ozonized olive oil were revealed during SEM observations. The combination of compounds that promote wound healing (hyaluronic acid, olive oil, ozone and calcium) with the antibacterial activity of the developed formula makes it a promising bionanocomposite for use as a topical dressing. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Inflammatory Skin Diseases)

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16 pages, 1568 KiB

Open AccessArticle

Quantitative Shotgun Proteomic Analysis of Bacteria after Overexpression of Recombinant Spider Miniature Spidroin, MaSp1

by Kathryn Randene, J Alexander Hoang Mendoza, Michael Ysit and Craig Vierra

Int. J. Mol. Sci. 2024, 25(6), 3556; https://doi.org/10.3390/ijms25063556 - 21 Mar 2024

Cited by 1 | Viewed by 1738

Abstract

Spider silk has extraordinary mechanical properties, displaying high tensile strength, elasticity, and toughness. Given the high performance of natural fibers, one of the long-term goals of the silk community is to manufacture large-scale synthetic spider silk. This process requires vast quantities of recombinant [...] Read more.

Spider silk has extraordinary mechanical properties, displaying high tensile strength, elasticity, and toughness. Given the high performance of natural fibers, one of the long-term goals of the silk community is to manufacture large-scale synthetic spider silk. This process requires vast quantities of recombinant proteins for wet-spinning applications. Attempts to synthesize large amounts of native size recombinant spidroins in diverse cell types have been unsuccessful. In these studies, we design and express recombinant miniature black widow MaSp1 spidroins in bacteria that incorporate the N-terminal and C-terminal domain (NTD and CTD), along with varying numbers of codon-optimized internal block repeats. Following spidroin overexpression, we perform quantitative analysis of the bacterial proteome to identify proteins associated with spidroin synthesis. Liquid chromatography with tandem mass spectrometry (LC MS/MS) reveals a list of molecular targets that are differentially expressed after enforced mini-spidroin production. This list included proteins involved in energy management, proteostasis, translation, cell wall biosynthesis, and oxidative stress. Taken together, the purpose of this study was to identify genes within the genome of Escherichia coli for molecular targeting to overcome bottlenecks that throttle spidroin overexpression in microorganisms. Full article

(This article belongs to the Special Issue Silk-Based Functional Materials: New Ways of Production, Properties and Applications)

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15 pages, 4902 KiB

Open AccessArticle

In Silico Description of the Direct Inhibition Mechanism of Endothelial Lipase by ANGPTL3

by Linda Montavoci, Omar Ben Mariem, Simona Saporiti, Tommaso Laurenzi, Luca Palazzolo, Alice Federica Ossoli, Uliano Guerrini, Laura Calabresi and Ivano Eberini

Int. J. Mol. Sci. 2024, 25(6), 3555; https://doi.org/10.3390/ijms25063555 - 21 Mar 2024

Viewed by 1152

Abstract

Angiopoietin-like protein 3 (ANGPTL3) is a plasmatic protein that plays a crucial role in lipoprotein metabolism by inhibiting the lipoprotein lipase (LPL) and the endothelial lipase (EL) responsible for the hydrolysis of phospholipids on high-density lipoprotein (HDL). Interest in developing new pharmacological therapies [...] Read more.

Angiopoietin-like protein 3 (ANGPTL3) is a plasmatic protein that plays a crucial role in lipoprotein metabolism by inhibiting the lipoprotein lipase (LPL) and the endothelial lipase (EL) responsible for the hydrolysis of phospholipids on high-density lipoprotein (HDL). Interest in developing new pharmacological therapies aimed at inhibiting ANGPTL3 has been growing due to the hypolipidemic and antiatherogenic profile observed in its absence. The goal of this study was the in silico characterization of the interaction between ANGPTL3 and EL. Because of the lack of any structural information on both the trimeric coiled-coil N-terminal domain of ANGPTL3 and the EL homodimer as well as data regarding their interactions, the first step was to obtain the three-dimensional model of these two proteins. The models were then refined via molecular dynamics (MD) simulations and used to investigate the interaction mechanism. The analysis of interactions in different docking poses and their refinement via MD allowed the identification of three specific glutamates of ANGPTL3 that recognize a positively charged patch on the surface of EL. These ANGPTL3 key residues, i.e., Glu154, Glu157, and Glu160, could form a putative molecular recognition site for EL. This study paves the way for future investigations aimed at confirming the recognition site and at designing novel inhibitors of ANGPTL3. Full article

(This article belongs to the Special Issue Computational Approaches for the Investigation of Complex Molecular Mechanisms 2.0)

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19 pages, 2715 KiB

Open AccessArticle

Plasma miR-203a-3p as a Novel Predictor of Dementia in Patients with Parkinson’s Disease

by Ya-Fang Hsu, Shau-Ping Lin, Yung-Tsai Chu, Yi-Tzang Tsai, Jing-Wen Huang, Frederick Kin Hing Phoa and Ruey-Meei Wu

Int. J. Mol. Sci. 2024, 25(6), 3554; https://doi.org/10.3390/ijms25063554 - 21 Mar 2024

Cited by 2 | Viewed by 1697

Abstract

The early detection of cognitive decline in Parkinson’s disease is important for providing drug therapy and non-pharmacological management. The circulating microRNAs present in plasma are promising biomarkers of PD with dementia (PDD) due to their critical roles in synaptic plasticity and the regulation [...] Read more.

The early detection of cognitive decline in Parkinson’s disease is important for providing drug therapy and non-pharmacological management. The circulating microRNAs present in plasma are promising biomarkers of PD with dementia (PDD) due to their critical roles in synaptic plasticity and the regulation of neurodegeneration-associated proteins. In this study, we aimed to identify plasma microRNAs that may differentiate PD with or without cognitive impairment. Global microRNA expression was obtained from a discovery set of 123 participants who were divided into four groups, namely normal controls (HC), PD with no dementia (PDND), PD with mild cognitive impairment (PD-MCI), and PDD, using next-generation sequencing. The BOLD selector was used for microRNA candidate selection. Six miRNAs, namely miR-203a-3p, miR-626, miR-662, miR-3182, miR-4274, and miR-4295, were clustered as potential candidates for use in identifying PDND from PD-MCI. Another independent cohort of 120 participants was further recruited in a validation step in order to detect candidate microRNAs via droplet digital PCR (ddPCR), which was used for its high sensitivity in detecting low miRNA concentrations. Our results show that the ratio of miR-203a-3p/miR-16-5p, in which miR-16-5p was used as a reference control miRNA, was significantly increased in PDD compared to that seen in PD-MCI and PDND individually, and was negatively correlated with the MoCA scores (r = −0.237, p = 0.024) in patients with PD. However, there was no significant difference in the ratio of miR-203a-3p/miR-16-5p between HC and PDND, PD-MCI, or PDD individually. The ROC curve of the logistic regression model, factoring in the variables of age, the ratio of miR-203a-3p/miR-16-5p, and the UPDRS III score, demonstrated an AUC of 0.883. Our findings suggest that the ratio of miR-203a-3p/miR-16-5p, used with age and motor score, could be a predictor of dementia among PD patients. Full article

(This article belongs to the Special Issue Circulating Biomarkers for the Diagnosis of Neurobiological Diseases)

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22 pages, 4200 KiB

Open AccessArticle

High- or Low-Yielding F₂ Progeny of Wheat Is Result of Specific TaCKX Gene Coexpression Patterns in Association with Grain Yield in Paternal Parent

by Karolina Szala, Marta Dmochowska-Boguta, Joanna Bocian, Wacław Orczyk and Anna Nadolska-Orczyk

Int. J. Mol. Sci. 2024, 25(6), 3553; https://doi.org/10.3390/ijms25063553 - 21 Mar 2024

Viewed by 955

Abstract

Members of the TaCKX gene family (GFM) encode oxidase/dehydrogenase cytokinin degrading enzymes (CKX), which play an important role in the homeostasis of phytohormones, affecting wheat development and productivity. Therefore, the objective of this investigation was to test how the expression patterns of the [...] Read more.

Members of the TaCKX gene family (GFM) encode oxidase/dehydrogenase cytokinin degrading enzymes (CKX), which play an important role in the homeostasis of phytohormones, affecting wheat development and productivity. Therefore, the objective of this investigation was to test how the expression patterns of the yield-related TaCKX genes and TaNAC2-5A (NAC2) measured in 7 days after pollination (DAP) spikes and the seedling roots of parents are inherited to apply this knowledge in the breeding process. The expression patterns of these genes were compared between parents and their F₂ progeny in crosses of one mother with different paterns of awnless cultivars and reciprocal crosses of awned and awnless lines. We showed that most of the genes tested in the 7 DAP spikes and seedling roots of the F₂ progeny showed paternal expression patterns in crosses of awnless cultivars as well as reciprocal crosses of awned and awnless lines. Consequently, the values of grain yield in the F₂ progeny were similar to the pater; however, the values of seedling root mass were similar to the mother or both parents. The correlation analysis of TaCKX GFMs and NAC2 in spikes and spikes per seedling roots reveals that the genes correlate with each other specifically with the pater and the F₂ progeny or the mother and the F₂ progeny, which shape phenotypic traits. The numbers of spikes and semi-empty spikes are mainly correlated with the specific coexpression of the TaCKX and NAC2 genes expressed in spikes or spikes per roots of the pater and F₂ progeny. Variable regression analysis of grain yield and root mass with TaCKX GFMs and NAC2 expressed in the tested tissues of five crosses revealed a significant dependency of these parameters on the mother and F₂ and/or the pater and F₂ progeny. We showed that the inheritance of yield-related traits depends on the specific cooperative expression of some TaCKX GFMs, in some crosses coupled with NAC2, and is strongly dependent on the genotypes used for the crosses. Indications for parental selection in the breeding of high-yielding lines are discussed. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetic Regulation of Crops)

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11 pages, 1638 KiB

Open AccessArticle

Development and Evaluation of an In-House Real-Time RT-PCR Targeting nsp10 Gene for SARS-CoV-2 Detection

by Cyril Chik-Yan Yip, Jane Hau-Ching Poon, Kit-Hang Leung, Wan-Mui Chan, Jonathan Daniel Ip, Allen Wing-Ho Chu, Vincent Chi-Chung Cheng, Kwok-Yung Yuen and Kelvin Kai-Wang To

Int. J. Mol. Sci. 2024, 25(6), 3552; https://doi.org/10.3390/ijms25063552 - 21 Mar 2024

Viewed by 1423

Abstract

The emergence of SARS-CoV-2 mutations poses significant challenges to diagnostic tests, as these mutations can reduce the sensitivity of commonly used RT-PCR assays. Therefore, there is a need to design diagnostic assays with multiple targets to enhance sensitivity. In this study, we identified [...] Read more.

The emergence of SARS-CoV-2 mutations poses significant challenges to diagnostic tests, as these mutations can reduce the sensitivity of commonly used RT-PCR assays. Therefore, there is a need to design diagnostic assays with multiple targets to enhance sensitivity. In this study, we identified a novel diagnostic target, the nsp10 gene, using nanopore sequencing. Firstly, we determined the analytical sensitivity and specificity of our COVID-19-nsp10 assay. The COVID-19-nsp10 assay had a limit of detection of 74 copies/mL (95% confidence interval: 48–299 copies/mL) and did not show cross-reactivity with other respiratory viruses. Next, we determined the diagnostic performance of the COVID-19-nsp10 assay using 261 respiratory specimens, including 147 SARS-CoV-2-positive specimens belonging to the ancestral strain and Alpha, Beta, Gamma, Delta, Mu, Eta, Kappa, Theta and Omicron lineages. Using a LightMix E-gene RT-PCR assay as the reference method, the diagnostic sensitivity and specificity of the COVID-19-nsp10 assay were found to be 100%. The median Cp values for the LightMix E-gene RT-PCR and our COVID-19-nsp10 RT-PCR were 22.48 (range: 12.95–36.60) and 25.94 (range 16.37–36.87), respectively. The Cp values of the COVID-19-nsp10 RT-PCR assay correlated well with those of the LightMix E-gene RT-PCR assay (Spearman’s ρ = 0.968; p < 0.0001). In conclusion, nsp10 is a suitable target for a SARS-CoV-2 RT-PCR assay. Full article

(This article belongs to the Special Issue Molecular Insights into Infectious Diseases)

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19 pages, 5050 KiB

Open AccessArticle

Evolution of the WRKY Family in Angiosperms and Functional Diversity under Environmental Stress

by Weihuang Wu, Jinchang Yang, Niu Yu, Rongsheng Li, Zaixiang Yuan, Jisen Shi and Jinhui Chen

Int. J. Mol. Sci. 2024, 25(6), 3551; https://doi.org/10.3390/ijms25063551 - 21 Mar 2024

Cited by 2 | Viewed by 1293

Abstract

The transcription factor is an essential factor for regulating the responses of plants to external stimuli. The WRKY protein is a superfamily of plant transcription factors involved in response to various stresses (e.g., cold, heat, salt, drought, ions, pathogens, and insects). During angiosperm [...] Read more.

The transcription factor is an essential factor for regulating the responses of plants to external stimuli. The WRKY protein is a superfamily of plant transcription factors involved in response to various stresses (e.g., cold, heat, salt, drought, ions, pathogens, and insects). During angiosperm evolution, the number and function of WRKY transcription factors constantly change. After suffering from long-term environmental battering, plants of different evolutionary statuses ultimately retained different numbers of WRKY family members. The WRKY family of proteins is generally divided into three large categories of angiosperms, owing to their conserved domain and three-dimensional structures. The WRKY transcription factors mediate plant adaptation to various environments via participating in various biological pathways, such as ROS (reactive oxygen species) and hormone signaling pathways, further regulating plant enzyme systems, stomatal closure, and leaf shrinkage physiological responses. This article analyzed the evolution of the WRKY family in angiosperms and its functions in responding to various external environments, especially the function and evolution in Magnoliaceae plants. It helps to gain a deeper understanding of the evolution and functional diversity of the WRKY family and provides theoretical and experimental references for studying the molecular mechanisms of environmental stress. Full article

(This article belongs to the Special Issue Molecular Advances in Abiotic Stress Signaling in Plants: Focus on Atmospheric Stressors)

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15 pages, 2003 KiB

Open AccessReview

Have All of the Phytohormonal Properties of Melatonin Been Verified?

by Woong June Park

Int. J. Mol. Sci. 2024, 25(6), 3550; https://doi.org/10.3390/ijms25063550 - 21 Mar 2024

Cited by 6 | Viewed by 1227

Abstract

Melatonin is a ubiquitous regulator in plants and performs a variety of physiological roles, including resistance to abiotic stress, regulation of growth and development, and enhancement of plant immunity. Melatonin exhibits the characteristics of a phytohormone with its pleiotropic effects, biosynthesis, conjugation, catabolism, [...] Read more.

Melatonin is a ubiquitous regulator in plants and performs a variety of physiological roles, including resistance to abiotic stress, regulation of growth and development, and enhancement of plant immunity. Melatonin exhibits the characteristics of a phytohormone with its pleiotropic effects, biosynthesis, conjugation, catabolism, effective concentration, and the shape and location of its dose–response curves. In addition, CAND2/PMTR1, a phytomelatonin receptor candidate belonging to the G protein-coupled receptors (GPCRs), supports the concept of melatonin as a phytohormone. However, the biochemistry of plant melatonin receptors needs to be further characterized. In particular, some of the experimental findings to date cannot be explained by known GPCR signaling mechanisms, so further studies are needed to explore the possibility of novel signaling mechanisms. Full article

(This article belongs to the Special Issue The Role of Melatonin in Plants 2.0)

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16 pages, 2346 KiB

Open AccessArticle

Association of Blast Exposure in Military Breaching with Intestinal Permeability Blood Biomarkers Associated with Leaky Gut

by Qingkun Liu, Zhaoyu Wang, Shengnan Sun, Jeffrey Nemes, Lisa A. Brenner, Andrew Hoisington, Maciej Skotak, Christina R. LaValle, Yongchao Ge, Walter Carr and Fatemeh Haghighi

Int. J. Mol. Sci. 2024, 25(6), 3549; https://doi.org/10.3390/ijms25063549 - 21 Mar 2024

Cited by 4 | Viewed by 3660

Abstract

Injuries and subclinical effects from exposure to blasts are of significant concern in military operational settings, including tactical training, and are associated with self-reported concussion-like symptomology and physiological changes such as increased intestinal permeability (IP), which was investigated in this study. Time-series gene [...] Read more.

Injuries and subclinical effects from exposure to blasts are of significant concern in military operational settings, including tactical training, and are associated with self-reported concussion-like symptomology and physiological changes such as increased intestinal permeability (IP), which was investigated in this study. Time-series gene expression and IP biomarker data were generated from “breachers” exposed to controlled, low-level explosive blast during training. Samples from 30 male participants at pre-, post-, and follow-up blast exposure the next day were assayed via RNA-seq and ELISA. A battery of symptom data was also collected at each of these time points that acutely showed elevated symptom reporting related to headache, concentration, dizziness, and taking longer to think, dissipating ~16 h following blast exposure. Evidence for bacterial translocation into circulation following blast exposure was detected by significant stepwise increase in microbial diversity (measured via alpha-diversity p = 0.049). Alterations in levels of IP protein biomarkers (i.e., Zonulin, LBP, Claudin-3, I-FABP) assessed in a subset of these participants (n = 23) further evidenced blast exposure associates with IP. The observed symptom profile was consistent with mild traumatic brain injury and was further associated with changes in bacterial translocation and intestinal permeability, suggesting that IP may be linked to a decrease in cognitive functioning. These preliminary findings show for the first time within real-world military operational settings that exposures to blast can contribute to IP. Full article

(This article belongs to the Special Issue Blast-Induced Neurotrauma: Molecular Mechanisms Supported by Comparative Experimental and Clinical Findings)

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6 pages, 225 KiB

Open AccessEditorial

Special Issue “COVID-19 Coagulopathy: Advances on Pathophysiology and Therapies”

by Eliza Russu, Emil-Marian Arbănaşi and Alexandru Șchiopu

Int. J. Mol. Sci. 2024, 25(6), 3548; https://doi.org/10.3390/ijms25063548 - 21 Mar 2024

Cited by 1 | Viewed by 1098

Abstract

The Special Issue on COVID-19 coagulopathy initiated one year ago aimed to shed light on the mechanisms underlying the changes in the coagulation status making SARS-CoV-2 infection such a tough adversary for every one of the medical specialties encountering it, along with overseeing [...] Read more.

The Special Issue on COVID-19 coagulopathy initiated one year ago aimed to shed light on the mechanisms underlying the changes in the coagulation status making SARS-CoV-2 infection such a tough adversary for every one of the medical specialties encountering it, along with overseeing the therapeutic applications derived from the current understanding of these mechanisms [...] Full article

(This article belongs to the Special Issue COVID-19 Coagulopathy: Advances on Pathophysiology and Therapies)

13 pages, 1637 KiB

Open AccessArticle

Expression of E-Cadherin and N-Cadherin in the Endocervix as a Predictive Factor in Patients with Endometrial Cancer

by Karolina Frąszczak, Bartłomiej Barczyński, Bożydar Tylus and Wiesława Bednarek

Int. J. Mol. Sci. 2024, 25(6), 3547; https://doi.org/10.3390/ijms25063547 - 21 Mar 2024

Viewed by 1251

Abstract

Endometrial cancer (EC) is the most common gynecological malignancy. This study aimed to evaluate the expression of E-cadherin and N-cadherin in primary endometrial lesions and the endocervix in patients with EC to identify noninvasive predictive factors. In this single-center retrospective study, data on [...] Read more.

Endometrial cancer (EC) is the most common gynecological malignancy. This study aimed to evaluate the expression of E-cadherin and N-cadherin in primary endometrial lesions and the endocervix in patients with EC to identify noninvasive predictive factors. In this single-center retrospective study, data on 101 patients who underwent surgery for EC were collected. The immunohistochemical expression of E-cadherin and N-cadherin was assessed depending on the tumor grade, location, and cell differentiation. Correlations between E-cadherin and N-cadherin levels in the endocervix and the primary tumor were determined. The degree of histological tumor differentiation significantly affected E-cadherin expression (p = 0.04) but had no impact on N-cadherin levels. In type II EC, the expression of both cadherins in the tumor tissue differed from their endocervical levels. The expression of E-cadherin differed significantly between the endocervix (p < 0.001) and the tumor (p = 0.001), depending on the type of EC. The expression of E-cadherin was related to the N-cadherin level only in the endocervix in patients with type II EC (p = 0.02). E-cadherin and N-cadherin were expressed in the endocervix in patients with EC. The expression of cadherins, determined during cervical cytology, may be a valuable clinical marker of EC. Full article

(This article belongs to the Section Molecular Oncology)

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22 pages, 3086 KiB

Open AccessArticle

Modeling Lysosomal Storage Disorders in an Innovative Way: Establishment and Characterization of Stem Cell Lines from Human Exfoliated Deciduous Teeth of Mucopolysaccharidosis Type II Patients

by Sofia Carvalho, Juliana Inês Santos, Luciana Moreira, Ana Joana Duarte, Paulo Gaspar, Hugo Rocha, Marisa Encarnação, Diogo Ribeiro, Matilde Barbosa Almeida, Mariana Gonçalves, Hugo David, Liliana Matos, Olga Amaral, Luísa Diogo, Sara Ferreira, Constança Santos, Esmeralda Martins, Maria João Prata, Luís Pereira de Almeida, Sandra Alves and Maria Francisca Coutinho Show full author list Hide full author list

Int. J. Mol. Sci. 2024, 25(6), 3546; https://doi.org/10.3390/ijms25063546 - 21 Mar 2024

Viewed by 1286

Abstract

Among the many lysosomal storage disorders (LSDs) that would benefit from the establishment of novel cell models, either patient-derived or genetically engineered, is mucopolysaccharidosis type II (MPS II). Here, we present our results on the establishment and characterization of two MPS II patient-derived [...] Read more.

Among the many lysosomal storage disorders (LSDs) that would benefit from the establishment of novel cell models, either patient-derived or genetically engineered, is mucopolysaccharidosis type II (MPS II). Here, we present our results on the establishment and characterization of two MPS II patient-derived stem cell line(s) from deciduous baby teeth. To the best of our knowledge, this is the first time a stem cell population has been isolated from LSD patient samples obtained from the dental pulp. Taking into account our results on the molecular and biochemical characterization of those cells and the fact that they exhibit visible and measurable disease phenotypes, we consider these cells may qualify as a valuable disease model, which may be useful for both pathophysiological assessments and in vitro screenings. Ultimately, we believe that patient-derived dental pulp stem cells (DPSCs), particularly those isolated from human exfoliated deciduous teeth (SHEDs), may represent a feasible alternative to induced pluripotent stem cells (iPSCs) in many labs with standard cell culture conditions and limited (human and economic) resources. Full article

(This article belongs to the Special Issue The Lysosome in Human Health and Diseases)

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15 pages, 1325 KiB

Open AccessArticle

Metabolomics of Plasma in XLH Patients with Arterial Hypertension: New Insights into the Underlying Mechanisms

by Luis Carlos López-Romero, José Jesús Broseta, Marta Roca-Marugán, Juan R. Muñoz-Castañeda, Agustín Lahoz and Julio Hernández-Jaras

Int. J. Mol. Sci. 2024, 25(6), 3545; https://doi.org/10.3390/ijms25063545 - 21 Mar 2024

Cited by 1 | Viewed by 1477

Abstract

X-linked hypophosphatemia (XLH) is a rare genetic disorder that increases fibroblast growth factor 23 (FGF23). XLH patients have an elevated risk of early-onset hypertension. The precise factors contributing to hypertension in XLH patients have yet to be identified. A multicenter cross-sectional study of [...] Read more.

X-linked hypophosphatemia (XLH) is a rare genetic disorder that increases fibroblast growth factor 23 (FGF23). XLH patients have an elevated risk of early-onset hypertension. The precise factors contributing to hypertension in XLH patients have yet to be identified. A multicenter cross-sectional study of adult patients diagnosed with XLH. Metabolomic analysis was performed using ultra-performance liquid chromatography (UPLC) coupled to a high-resolution mass spectrometer. Twenty subjects were included, of which nine (45%) had hypertension. The median age was 44 years. Out of the total, seven (35%) subjects had a family history of hypertension. No statistically significant differences were found between both groups for nephrocalcinosis or hyperparathyroidism. Those with hypertension exhibited significantly higher levels of creatinine (1.08 ± 0.31 mg/dL vs. 0.78 ± 0.19 mg/dL; p = 0.01) and LDL-C (133.33 ± 21.92 mg/dL vs. 107.27 ± 20.12 mg/dL, p = 0.01). A total of 106 metabolites were identified. Acetylcarnitine (p = 0.03), pyruvate p = (0.04), ethanolamine (p = 0.03), and butyric acid (p = 0.001) were significantly different between both groups. This study is the first to examine the metabolomics of hypertension in patients with XLH. We have identified significant changes in specific metabolites that shed new light on the potential mechanisms of hypertension in XLH patients. These findings could lead to new studies identifying associated biomarkers and developing new diagnostic approaches for XLH patients. Full article

(This article belongs to the Collection 21st Anniversary of IJMS: Advances in Molecular Endocrinology and Metabolism)

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22 pages, 5598 KiB

Open AccessArticle

Gender-Specific Renoprotective Pathways in αMUPA Transgenic Mice Subjected to Acute Kidney Injury

by Heba Abd Alkhaleq, Shadi Hamoud, Israel Hacker, Tony Karram, Ahmad Fokra, Aviva Kabala and Zaid Abassi

Int. J. Mol. Sci. 2024, 25(6), 3544; https://doi.org/10.3390/ijms25063544 - 21 Mar 2024

Cited by 1 | Viewed by 1247

Abstract

Acute kidney injury (AKI) is a serious health concern with high morbidity and high mortality worldwide. Recently, sexual dimorphism has become increasingly recognized as a factor influencing the severity of the disease. This study explores the gender-specific renoprotective pathways in αMUPA transgenic mice [...] Read more.

Acute kidney injury (AKI) is a serious health concern with high morbidity and high mortality worldwide. Recently, sexual dimorphism has become increasingly recognized as a factor influencing the severity of the disease. This study explores the gender-specific renoprotective pathways in αMUPA transgenic mice subjected to AKI. αMUPA transgenic male and female mice were subjected to ischemia–reperfusion (I/R)-AKI in the presence or absence of orchiectomy, oophorectomy, and L-NAME administration. Blood samples and kidneys were harvested 48 h following AKI for the biomarkers of kidney function, renal injury, inflammatory response and intracellular pathway sensing of or responding to AKI. Our findings show differing responses to AKI, where female αMUPA mice were remarkably protected against AKI as compared with males, as was evident by the lower SCr and BUN, normal renal histologically and attenuated expression of NGAL and KIM-1. Moreover, αMUPA females did not show a significant change in the renal inflammatory and fibrotic markers following AKI as compared with wild-type (WT) mice and αMUPA males. Interestingly, oophorectomized females eliminated the observed resistance to renal injury, highlighting the central protective role of estrogen. Correspondingly, orchiectomy in αMUPA males mitigated their sensitivity to renal damage, thereby emphasizing the devastating effects of testosterone. Additionally, treatment with L-NAME proved to have significant deleterious impacts on the renal protective mediators, thereby underscoring the involvement of eNOS. In conclusion, gender-specific differences in the response to AKI in αMUPA mice include multifaceted and keen interactions between the sex hormones and key biochemical mediators (such as estrogen, testosterone and eNOS). These novel findings shed light on the renoprotective pathways and mechanisms, which may pave the way for development of therapeutic interventions. Full article

(This article belongs to the Special Issue Pathophysiology of Acute Kidney Injury)

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20 pages, 21642 KiB

Open AccessArticle

Anatomical Anal Stenosis after PPH: Insights from a Retrospective Study and Rat Model

by Chia-Cheng Wen, Shih-Ming Huang and Yi-Wen Wang

Int. J. Mol. Sci. 2024, 25(6), 3543; https://doi.org/10.3390/ijms25063543 - 21 Mar 2024

Viewed by 1346

Abstract

High-grade hemorrhoids are usually recommended to receive operational treatments. However, these traditional surgeries are associated with severe postoperative pain. A procedure for prolapse and hemorrhoids (PPH), a circular staple device, has been developed to improve short-term outcomes, including reducing the severity of postoperative [...] Read more.

High-grade hemorrhoids are usually recommended to receive operational treatments. However, these traditional surgeries are associated with severe postoperative pain. A procedure for prolapse and hemorrhoids (PPH), a circular staple device, has been developed to improve short-term outcomes, including reducing the severity of postoperative pain. PPH, compared to conventional surgery, has been associated with the incidence of anatomical anal stenosis. The causes of stenosis after PPH are not yet clear. We first analyzed the complications of our patients with PPH, and then developed a rat model to verify the tension force of PPH using Hematoxylin-eosin, Masson’s trichrome, immunohistochemistry, and immunofluorescence staining. Our clinical data showed that PPH significantly improved postoperative pain, but that it resulted in higher incidences of complications, including anal stenosis, than hemorrhoidectomy. We simulated the status of PPH and developed a rat model to verify PPH’s tension force, including the scarring area and the deposition of proinflammatory factors, angiogenic factors, and fibrotic factors. The tension wound histological data showed more extensive granulation tissue and inflammatory cell infiltration and a thicker epidermis than the control group on day 12 post-operation and tension treatment. In addition to IL-1β and IL-10 cytokines on day 3 and IL-1β, IL-6, and IL-10 cytokines on day 12 post-operation in the tension group, two angiogenic factors, CD31 and VEGF-A, were found to have a more significant expression on day 7 post-operation in the tension group. The mean scar area was larger and the distribution of fibrotic proteins (collagen 1, α-SMA, CTGF, and MMP2) in the tension group was significantly broader than in the control on day 12 post-operation and tension treatment. Based on the findings of our animal model, the development of a lesser tensile force for PPH to decrease the deposition of proinflammatory factors, angiogenic factors, and fibrotic factors is urgently required. Full article

(This article belongs to the Topic Animal Models of Human Disease 2.0)

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14 pages, 3628 KiB

Open AccessArticle

PPR596 Is Required for nad2 Intron Splicing and Complex I Biogenesis in Arabidopsis

by Aqib Sayyed, Baoyin Chen, Yong Wang, Shi-Kai Cao and Bao-Cai Tan

Int. J. Mol. Sci. 2024, 25(6), 3542; https://doi.org/10.3390/ijms25063542 - 21 Mar 2024

Cited by 1 | Viewed by 1282

Abstract

Mitochondria are essential organelles that generate energy via oxidative phosphorylation. Plant mitochondrial genome encodes some of the respiratory complex subunits, and these transcripts require accurate processing, including C-to-U RNA editing and intron splicing. Pentatricopeptide repeats (PPR) proteins are involved in various organellar RNA [...] Read more.

Mitochondria are essential organelles that generate energy via oxidative phosphorylation. Plant mitochondrial genome encodes some of the respiratory complex subunits, and these transcripts require accurate processing, including C-to-U RNA editing and intron splicing. Pentatricopeptide repeats (PPR) proteins are involved in various organellar RNA processing events. PPR596, a P-type PPR protein, was previously identified to function in the C-to-U editing of mitochondrial rps3 transcripts in Arabidopsis. Here, we demonstrate that PPR596 functions in the cis-splicing of nad2 intron 3 in mitochondria. Loss of the PPR596 function affects the editing at rps3eU1344SS, impairs nad2 intron 3 splicing and reduces the mitochondrial complex I’s assembly and activity, while inducing alternative oxidase (AOX) gene expression. This defect in nad2 intron splicing provides a plausible explanation for the slow growth of the ppr595 mutants. Although a few P-type PPR proteins are involved in RNA C-to-U editing, our results suggest that the primary function of PPR596 is intron splicing. Full article

(This article belongs to the Section Molecular Plant Sciences)

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19 pages, 18203 KiB

Open AccessArticle

The RopGEF Gene Family and Their Potential Roles in Responses to Abiotic Stress in Brassica rapa

by Meiqi Zhang, Xiaoyu Wu, Luhan Chen, Lin Yang, Xiaoshuang Cui and Yunyun Cao

Int. J. Mol. Sci. 2024, 25(6), 3541; https://doi.org/10.3390/ijms25063541 - 21 Mar 2024

Cited by 1 | Viewed by 1350

Abstract

Guanine nucleotide-exchange factors (GEFs) genes play key roles in plant root and pollen tube growth, phytohormone responses, and abiotic stress responses. RopGEF genes in Brassica rapa have not yet been explored. Here, GEF genes were found to be distributed across eight [...] Read more.

Guanine nucleotide-exchange factors (GEFs) genes play key roles in plant root and pollen tube growth, phytohormone responses, and abiotic stress responses. RopGEF genes in Brassica rapa have not yet been explored. Here, GEF genes were found to be distributed across eight chromosomes in B. rapa and were classified into three subfamilies. Promoter sequence analysis of BrRopGEFs revealed the presence of cis-elements characteristic of BrRopGEF promoters, and these cis-elements play a role in regulating abiotic stress tolerance and stress-related hormone responses. Organ-specific expression profiling demonstrated that BrRopGEFs were ubiquitously expressed in all organs, especially the roots, suggesting that they play a role in diverse biological processes. Gene expression analysis revealed that the expression of BrRopGEF13 was significantly up-regulated under osmotic stress and salt stress. RT-qPCR analysis revealed that the expression of BrRopGEF13 was significantly down-regulated under various types of abiotic stress. Protein–protein interaction (PPI) network analysis revealed interactions between RopGEF11, the homolog of BrRopGEF9, and the VPS34 protein in Arabidopsis thaliana, as well as interactions between AtRopGEF1, the homolog of BrRopGEF13 in Arabidopsis, and the ABI1, HAB1, PP2CA, and CPK4 proteins. VPS34, ABI1, HAB1, PP2CA, and CPK4 have previously been shown to confer resistance to unfavorable environments. Overall, our findings suggest that BrRopGEF9 and BrRopGEF13 play significant roles in regulating abiotic stress tolerance. These findings will aid future studies aimed at clarifying the functional characteristics of BrRopGEFs. Full article

(This article belongs to the Special Issue Regulatory Mechanism and Network of Abiotic Stress-Response in Plants 2.0)

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24 pages, 2037 KiB

Open AccessReview

Interactions between Gut Microbiota and Oral Antihyperglycemic Drugs: A Systematic Review

by Nicoleta Mihaela Mindrescu, Cristian Guja, Viorel Jinga, Sorina Ispas, Antoanela Curici, Andreea Nelson Twakor and Anca Mihaela Pantea Stoian

Int. J. Mol. Sci. 2024, 25(6), 3540; https://doi.org/10.3390/ijms25063540 - 21 Mar 2024

Cited by 6 | Viewed by 2421

Abstract

The intestinal microbiota refers to the collection of microorganisms that exist in the human gut. It has been said that bacteria influence the development of metabolic diseases, such as diabetes mellitus, as they have roles in immunomodulation, protection against pathogens, blood vessel growth, [...] Read more.

The intestinal microbiota refers to the collection of microorganisms that exist in the human gut. It has been said that bacteria influence the development of metabolic diseases, such as diabetes mellitus, as they have roles in immunomodulation, protection against pathogens, blood vessel growth, repairing the intestinal wall, and the development of the neurological system. In this review, we look at the latest research regarding interactions between gut microbiota and oral antihyperglycemic drugs and we present data suggesting that the microbiome may help counteract the reduced glucose tolerance and insulin resistance associated with metabolic disorders. We found that antidiabetic drugs can have significant impacts on gut microbiota composition and function, potentially influencing both the efficacy and side effects of these medications. Additionally, we discovered that microbial-based therapeutics, including probiotics, prebiotics, and postbiotics, and fecal microbiota can be considered when discussing preventive measures and personalized treatment options for type 2 diabetes mellitus. Understanding how antidiabetic drugs modulate gut microbiota composition and function is essential for optimizing their therapeutic efficacy and minimizing potential adverse effects. The relationship between the gut microbiota and glycemic agents, not fully understood, is currently the subject of increasing research and discussion. It has been proven that the microbiome can impact the effectiveness of the medications, but further research in this field may uncover novel therapeutic strategies for diabetes and other metabolic disorders by targeting the gut microbiota. Full article

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

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23 pages, 2088 KiB

Open AccessReview

Unveiling the Hidden Regulators: The Impact of lncRNAs on Zoonoses

by Bojie Xu, Yujuan He, Ruicheng Yang, Junmin Li and Xiangru Wang

Int. J. Mol. Sci. 2024, 25(6), 3539; https://doi.org/10.3390/ijms25063539 - 21 Mar 2024

Cited by 1 | Viewed by 1720

Abstract

Zoonoses are diseases and infections naturally transmitted between humans and vertebrate animals. They form the dominant group of diseases among emerging infectious diseases and represent critical threats to global health security. This dilemma is largely attributed to our insufficient knowledge of the pathogenesis [...] Read more.

Zoonoses are diseases and infections naturally transmitted between humans and vertebrate animals. They form the dominant group of diseases among emerging infectious diseases and represent critical threats to global health security. This dilemma is largely attributed to our insufficient knowledge of the pathogenesis regarding zoonotic spillover. Long non-coding RNAs (lncRNAs) are transcripts with limited coding capacity. Recent technological advancements have enabled the identification of numerous lncRNAs in humans, animals, and even pathogens. An increasing body of literature suggests that lncRNAs function as key regulators in zoonotic infection. They regulate immune-related epigenetic, transcriptional, and post-transcriptional events across a broad range of organisms. In this review, we discuss the recent research progress on the roles of lncRNAs in zoonoses. We address the classification and regulatory mechanisms of lncRNAs in the interaction between host and zoonotic pathogens. Additionally, we explore the surprising function of pathogen-derived lncRNAs in mediating the pathogenicity and life cycle of zoonotic bacteria, viruses, and parasites. Understanding how these lncRNAs influence the zoonotic pathogenesis will provide important therapeutic insights to the prevention and control of zoonoses. Full article

(This article belongs to the Section Molecular Biology)

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21 pages, 3022 KiB

Open AccessReview

Role of Sensory Nerves in Pulmonary Fibrosis

by Charles E. Norton

Int. J. Mol. Sci. 2024, 25(6), 3538; https://doi.org/10.3390/ijms25063538 - 21 Mar 2024

Viewed by 1628

Abstract

Pulmonary fibrosis results from the deposition and proliferation of extracellular matrix components in the lungs. Despite being an airway disorder, pulmonary fibrosis also has notable effects on the pulmonary vasculature, with the development and severity of pulmonary hypertension tied closely to patient mortality. [...] Read more.

Pulmonary fibrosis results from the deposition and proliferation of extracellular matrix components in the lungs. Despite being an airway disorder, pulmonary fibrosis also has notable effects on the pulmonary vasculature, with the development and severity of pulmonary hypertension tied closely to patient mortality. Furthermore, the anatomical proximity of blood vessels, the alveolar epithelium, lymphatic tissue, and airway spaces highlights the need to identify shared pathogenic mechanisms and pleiotropic signaling across various cell types. Sensory nerves and their transmitters have a variety of effects on the various cell types within the lungs; however, their effects on many cell types and functions during pulmonary fibrosis have not yet been investigated. This review highlights the importance of gaining a new understanding of sensory nerve function in the context of pulmonary fibrosis as a potential tool to limit airway and vascular dysfunction. Full article

(This article belongs to the Special Issue Novel Insight into Pulmonary Vascular Disease)

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35 pages, 2685 KiB

Open AccessReview

Lipoprotein(a) and Atherosclerotic Cardiovascular Disease: Where Do We Stand?

by Georgios Tsioulos, Dimitris Kounatidis, Natalia G. Vallianou, Aikaterini Poulaki, Evangelia Kotsi, Gerasimos Socrates Christodoulatos, Dimitrios Tsilingiris, Irene Karampela, Alexandros Skourtis and Maria Dalamaga

Int. J. Mol. Sci. 2024, 25(6), 3537; https://doi.org/10.3390/ijms25063537 - 21 Mar 2024

Cited by 1 | Viewed by 2517

Abstract

Lipoprotein(a) [Lp(a)] consists of a low-density lipoprotein-like molecule and an apolipoprotein(a) [apo(a)] particle. Lp(a) has been suggested to be an independent risk factor of atherosclerotic cardiovascular disease (ASCVD). Lp(a) plasma levels are considered to be 70–90% genetically determined through the codominant expression of [...] Read more.

Lipoprotein(a) [Lp(a)] consists of a low-density lipoprotein-like molecule and an apolipoprotein(a) [apo(a)] particle. Lp(a) has been suggested to be an independent risk factor of atherosclerotic cardiovascular disease (ASCVD). Lp(a) plasma levels are considered to be 70–90% genetically determined through the codominant expression of the LPA gene. Therefore, Lp(a) levels are almost stable during an individual’s lifetime. This lifelong stability, together with the difficulties in measuring Lp(a) levels in a standardized manner, may account for the scarcity of available drugs targeting Lp(a). In this review, we synopsize the latest data regarding the structure, metabolism, and factors affecting circulating levels of Lp(a), as well as the laboratory determination measurement of Lp(a), its role in the pathogenesis of ASCVD and thrombosis, and the potential use of various therapeutic agents targeting Lp(a). In particular, we discuss novel agents, such as antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs) that are currently being developed and target Lp(a). The promising role of muvalaplin, an oral inhibitor of Lp(a) formation, is then further analyzed. Full article

(This article belongs to the Special Issue Lipid Metabolism and Signaling in Tumors and Cerebrovascular Diseases 2.0)

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19 pages, 4981 KiB

Open AccessReview

Noscapine and Apoptosis in Breast and Other Cancers

by Gloria M. Calaf, Leodan A. Crispin and Edwin O. Quisbert-Valenzuela

Int. J. Mol. Sci. 2024, 25(6), 3536; https://doi.org/10.3390/ijms25063536 - 21 Mar 2024

Cited by 3 | Viewed by 2117

Abstract

Breast cancer is the second leading contributor to the age-standardized mortality rate, for both sexes and all ages worldwide. In Europe and the United States, it is the second leading cause of mortality, with an incidence rate of about 2.6 million cases per [...] Read more.

Breast cancer is the second leading contributor to the age-standardized mortality rate, for both sexes and all ages worldwide. In Europe and the United States, it is the second leading cause of mortality, with an incidence rate of about 2.6 million cases per year. Noscapine, a well-known alkaloid used as a cough suppressant, demonstrated anti-tumor effects by triggering apoptosis in various cancer cell lines and has the potential to become another ally against breast, ovarian, colon, and gastric cancer, among other types of malignancy. Apoptosis plays a crucial role in the treatment of cancer. Noscapine affected BAX, CASP8, CASP9, NFKBIA, and RELA gene and protein expression in the MCF-7 and MDA-MB-231 cell lines. Gene expression was higher in tumor than in normal tissue, including the BAX expression levels in lung, ovary, endometrium, colon, stomach, and glioblastoma patients; BCL2L1 expression in endometrium, colon, and stomach patients; CASP8 gene expression levels in lung, endometrium, colon, stomach, and glioblastoma patients; RELA in colon, stomach, and glioblastoma patients; and NFKBIA in glioblastoma patients. It can be concluded that noscapine affected genes and proteins related to apoptosis in cancer cell lines and several types of cancer patients. Full article

(This article belongs to the Section Molecular Biology)

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18 pages, 1437 KiB

Open AccessArticle

Identification of an Intravenous Injectable NK1 Receptor Antagonist for Use in Traumatic Brain Injury

by Robert Vink and Alan Nimmo

Int. J. Mol. Sci. 2024, 25(6), 3535; https://doi.org/10.3390/ijms25063535 - 21 Mar 2024

Cited by 1 | Viewed by 1329

Abstract

Traumatic brain injuries represent a leading cause of death and disability in the paediatric and adult populations. Moderate-to-severe injuries are associated with blood–brain barrier dysfunction, the development of cerebral oedema, and neuroinflammation. Antagonists of the tachykinin NK1 receptor have been proposed as potential [...] Read more.

Traumatic brain injuries represent a leading cause of death and disability in the paediatric and adult populations. Moderate-to-severe injuries are associated with blood–brain barrier dysfunction, the development of cerebral oedema, and neuroinflammation. Antagonists of the tachykinin NK1 receptor have been proposed as potential agents for the post-injury treatment of TBI. We report on the identification of EUC-001 as a potential clinical candidate for development as a novel TBI therapy. EUC-001 is a selective NK1 antagonist with a high affinity for the human NK1 receptor (Ki 5.75 × 10⁻¹⁰ M). It has sufficient aqueous solubility to enable intravenous administration, whilst still retaining good CNS penetration as evidenced by its ability to inhibit the gerbil foot-tapping response. Using an animal model of TBI, the post-injury administration of EUC-001 was shown to restore BBB function in a dose-dependent manner. EUC-001 was also able to ameliorate cerebral oedema. These effects were associated with a significant reduction in post-TBI mortality. In addition, EUC-001 was able to significantly reduce functional deficits, both motor and cognitive, that normally follow a severe injury. EUC-001 is proposed as an ideal candidate for clinical development for TBI. Full article

(This article belongs to the Special Issue Molecular Mechanisms and Physiology Associated with the Blood–Brain Barrier)

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15 pages, 602 KiB

Open AccessArticle

Comparative Analyses of Targeted Myeloid Cancer Next-Generation Sequencing Panel in Fresh Blood, Bone Marrow and FFPE Material

by Andrea Daniela Hobeck, Sophia Wendt, Saskia Krohn, Gudrun Knuebel, Stephan Bartels, Elisa Schipper, Christian Junghanss and Hugo Murua Escobar

Int. J. Mol. Sci. 2024, 25(6), 3534; https://doi.org/10.3390/ijms25063534 - 21 Mar 2024

Viewed by 1317

Abstract

Next-generation sequencing is a vital tool for personalized diagnostics and therapies in cancer. Despite numerous advantages, the method depends on multiple parameters regarding the sample material, e.g., sample fixation. A panel’s ability to ensure balanced pre-amplification of the regions of interest is challenging, [...] Read more.

Next-generation sequencing is a vital tool for personalized diagnostics and therapies in cancer. Despite numerous advantages, the method depends on multiple parameters regarding the sample material, e.g., sample fixation. A panel’s ability to ensure balanced pre-amplification of the regions of interest is challenging, especially in targeted sequencing approaches, but of significant importance to its applicability across hematological malignancies and solid tumors. This study comparatively evaluated the technical performance of the commercially available Oncomine^TM Myeloid Panel in fresh and Formalin-fixed paraffin-embedded (FFPE) material by using an Ion Torrent™ Personal Genome Machine™ System and Ion GeneStudio S5 System platform. In total, 114 samples were analyzed, including 55 fresh materials and 59 FFPE samples. Samples were sequenced with a minimum of one million reads. Amplicons with coverage below 400 reads were classified as underperforming. In fresh material, 49/526 amplicons were identified as performing insufficiently, corresponding with 18 genes. Using FFPE material, 103/526 amplicons underperformed. Independent of input material, regions in 27 genes, including ASXL1, BCOR and BRAF, did not match quality parameters. Subsequently, exemplary mutations were extracted from the Catalogue of Somatic Mutations in Cancer database. This technical evaluation of the Oncomine^TM Myeloid Panel identified amplicons that do not achieve adequate coverage levels and which need to be considered when interpreting sequencing. Full article

(This article belongs to the Special Issue Next-Generation Sequencing and Whole-Genome Sequencing in Molecular Research)

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