International Journal of Molecular Sciences

10 pages, 10345 KiB

Open AccessArticle

Pyridazino-1,3a,6a-Triazapentalenes as Versatile Fluorescent Probes: Impact of Their Post-Functionalization and Application for Cellular Imaging

by Doina Sirbu, Nicolas Chopin, Ivana Martinić, Moussa Ndiaye, Svetlana V. Eliseeva, Marie-Aude Hiebel, Stéphane Petoud and Franck Suzenet

Int. J. Mol. Sci. 2021, 22(12), 6645; https://doi.org/10.3390/ijms22126645 - 21 Jun 2021

Cited by 8 | Viewed by 2707

Abstract

Pyridazino-1,3a,6a-triazapentalenes (PyTAP) are compact fused 6/5/5 tricyclic scaffolds which exhibit promising fluorescent properties. Chemically stable, they can be post-functionalized using standard Pd-catalyzed cross-coupling chemistry. Several original PyTAP bearing additional unsaturated substituents in positions 2 and 8 were synthetized and their spectroscopic properties analyzed. [...] Read more.

Pyridazino-1,3a,6a-triazapentalenes (PyTAP) are compact fused 6/5/5 tricyclic scaffolds which exhibit promising fluorescent properties. Chemically stable, they can be post-functionalized using standard Pd-catalyzed cross-coupling chemistry. Several original PyTAP bearing additional unsaturated substituents in positions 2 and 8 were synthetized and their spectroscopic properties analyzed. They have been successfully tested as fluorescent probes for cellular imaging. Full article

(This article belongs to the Special Issue Advanced Fluorescent Probes for Structural and Functional Imaging of Biological Systems 2.0)

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Images obtained from epifluorescence microscopy experiments on living HeLa cells. (Top) after 1 h and 30 min of incubation with 30 µM solution of the 3a fluorescent probe. (Bottom) Untreated cells as a control. (A) Brightfield. (B) Fluorescence. λex: 485 nm band pass 20 nm filter, λem: 525 nm band pass 50 nm, τexp: 300 ms. (C) Merged. 40× objective. Full article ">Figure 2
Results of epifluorescence microscopy experiments on living HeLa cells. (Top) after 1 h and 30 min of incubation with a 210 µM solution of the 4i probe. (Bottom) Untreated cells as a control. (A) Brightfield. (B) Fluorescence. λex: 417 nm band pass 60 nm filter, λem: 536 nm band pass 40 nm, τexp: 500 ms. (C) Merged. 40× objective. Full article ">Figure 3
Images obtained from photobleaching experiments. HeLa cells incubated (top) during 1 h and 30 min with a 30 µM solution of the 3a or (bottom) during 30 min with a 50 nM LysoTracker Green DND-26 after exposure to a continuous excitation light selected with a 485 nm (band pass 20 nm filter) collected at different times: (A) 0 s, (B) 25 s, (C) 45 s, (D) 100 s, (E) 185 s. The emission signal was collected with a 525 nm band pass 50 nm, τexp: 300 ms, 40× objective. Full article ">Figure 4
Images collected during photobleaching experiments. HeLa cells incubated (top) during 1h and 30 min with a 210 µM solution of the 4i probe or (bottom) during 30 min with 50 nM LysoTracker Green DND-26 after exposure to a continuous excitation light selected with a 417 nm (band pass 60 nm filter) collected at different times: (A) 0 s, (B) 30 s, (C) 75 s, (D) 180 s, (E) 485 s. The emission signal was collected with a 536 nm band pass 54 nm, τexp: 500 ms, 63× objective. Full article ">Scheme 1
TAP and PyTAP scaffolds. Full article ">Scheme 2
(2a) Formation of 2- and 8-substituted PyTAP through Suzuki-Miyaura cross-coupling reactions. (2b) Formation of 2- and 8-substituted PyTAP through Sonogashira cross-coupling reactions. Full article ">Scheme 3
Introduction of ester (3a) and aminated (3b) groups through Sonogashira cross-coupling reactions. Introduction of ester (3c) group through a CuAAC reaction. Full article ">

17 pages, 4291 KiB

Open AccessArticle

Integrated Insight into the Molecular Mechanisms of Spontaneous Abortion during Early Pregnancy in Pigs

by Xupeng Zang, Ting Gu, Wenjing Wang, Chen Zhou, Yue Ding, Shengchen Gu, Zhiqian Xu, Yanshe Xie, Zicong Li, Gengyuan Cai, Bin Hu, Linjun Hong and Zhenfang Wu

Int. J. Mol. Sci. 2021, 22(12), 6644; https://doi.org/10.3390/ijms22126644 - 21 Jun 2021

Cited by 9 | Viewed by 3302

Abstract

Due to the high rate of spontaneous abortion (SAB) in porcine pregnancy, there is a major interest and concern on commercial pig farming worldwide. Whereas the perturbed immune response at the maternal–fetal interface is an important mechanism associated with the spontaneous embryo loss [...] Read more.

Due to the high rate of spontaneous abortion (SAB) in porcine pregnancy, there is a major interest and concern on commercial pig farming worldwide. Whereas the perturbed immune response at the maternal–fetal interface is an important mechanism associated with the spontaneous embryo loss in the early stages of implantation in porcine, data on the specific regulatory mechanism of the SAB at the end stage of the implantation remains scant. Therefore, we used high-throughput sequencing and bioinformatics tools to analyze the healthy and arresting endometrium on day 28 of pregnancy. We identified 639 differentially expressed lncRNAs (DELs) and 2357 differentially expressed genes (DEGs) at the end stage of implantation, and qRT-PCR was used to verify the sequencing data. Gene set variation analysis (GSVA), gene set enrichment analysis (GSEA), and immunohistochemistry analysis demonstrated weaker immune response activities in the arresting endometrium compared to the healthy one. Using the lasso regression analysis, we screened the DELs and constructed an immunological competitive endogenous RNA (ceRNA) network related to SAB, including 4 lncRNAs, 11 miRNAs, and 13 genes. In addition, Blast analysis showed the applicability of the constructed ceRNA network in different species, and subsequently determined HOXA-AS2 in pigs. Our study, for the first time, demonstrated that the SAB events at the end stages of implantation is associated with the regulation of immunobiological processes, and a specific molecular regulatory network was obtained. These novel findings may provide new insight into the possibility of increasing the litter size of sows, making pig breeding better and thus improving the efficiency of animal husbandry production. Full article

(This article belongs to the Special Issue Reproductive Immunology and Pregnancy 2.0)

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Flowchart of the study. The photograph of the embryos corresponds with the pattern diagrams, which demonstrate the healthy or arresting embryos at day 28 of pregnancy. Details of the methods and results are described later. Full article ">Figure 2
Identification and characterization of lncRNAs and mRNAs. (A) Distribution of the reads in different regions of the genome. (B) Screening of candidate novel lncRNAs. Three tools (CPC, CNCI, and PFAM) were used to analyze the coding potential of the lncRNAs, and the iterated lncRNAs were designated as candidate novel lncRNAs and used together with annotated lncRNAs for subsequent analysis. (C) Classification of the novel lncRNAs. (D) Distribution of lncRNAs and mRNAs in the genome. (E–G) Transcript length, exon number, and ORF length distribution of the lncRNAs and mRNAs. (H) Pie chart showing the percentage distribution of repeat sequences in the lncRNA and mRNA populations. (I,J) PCA and hierarchical clustering heatmap were used to check the differences between paired endometrial samples. Full article ">Figure 3
Screening and enrichment analysis of the differentially expressed lncRNAs (DELs) in AE compared with HE. (A) DELs expression profile by scatter plot. Each point represents one lncRNA. The red points represent upregulated lncRNAs while the blue points represent downregulated lncRNAs. (B) Hierarchical clustering heatmap of the DELs. The color scale is from −2.0 (blue, lower lncRNA expression level) to 2.0 (red, higher lncRNA expression level). Each row represents one lncRNA, and each column represents one sample. The red band on the left side of the heatmap represents clustering of the upregulated lncRNAs, and the green represents the downregulated lncRNAs. (C) Raincloud plot of the upregulated and downregulated DELs. (D) GO enrichment analysis of the DELs nearest target genes. (E) KEGG pathway analysis of the DELs nearest target genes. The different color represents the categories to which the KEGG pathway belongs. (F) Validation of the expression of genes using qRT-PCR. The relative expression level was normalized by log10. Full article ">Figure 4
Screening and enrichment analysis of the differentially expressed genes (DEGs) in AE compared with HE. (A) DEGs expression level analysis by scatter plot. Each point represents one gene. The red points represent upregulated genes while the blue points represent downregulated genes. (B) Hierarchical clustering heatmap of the DEGs. The color scale is from −2.0 (blue, lower gene expression level) to 2.0 (red, higher gene expression level). Each row represents one gene, and each column represents one sample. The red band on the left side of the heatmap represents the clustered upregulated genes, while the green represents downregulated gene clusters. (C) Raincloud plot of upregulated and downregulated DEGs. (D) GO enrichment analysis of the DEGs. (E) KEGG pathway analysis of the DEGs. The different color represents the categories to which the KEGG pathway belongs. (F) Validation of the expression of genes using qRT-PCR. The relative expression level was normalized by log10. Full article ">Figure 5
Weakened immunobiological activities in AE. (A) Gene set variation analysis (GSVA) demonstrated enrichment of the immunobiological processes in HE. Each row represents one biological process, and each column represents one sample. (B) Raincloud plot of the GSVA enrichment results. (C) Gene set enrichment analysis (GSEA) indicated a positive enrichment of two immunobiological processes (‘cell activation involved in immune response’ and ‘regulation of immune response’) in HE. The heatmap on the right shows the gene expression level in the two biological processes of enrichment. (D) Venn diagram of immune genes (IGs) and DEGs, the intersection indicates the differentially expressed genes related to immunity. (E) PPI network of IRDEGs visualized using Cytoscape. The size of the circle represents the degree of interaction between the genes. Immunohistochemical localization of CD44 in HE (F) and AE (G). CD44 expression was evident in HE, while almost not expressed in AE. CE: chorionic epithelium; GE: glandular epithelium; LE: luminal epithelium. Full article ">Figure 6
The immune-related endometrial spontaneous abortion (SAB) competitive endogenous RNA (ceRNA) network. (A) Results of the lasso regression analysis for 639 DELs. Ten-fold cross-validation was used to calculate the best lambda value that results in the minimum mean cross-validation error. The red dot represents partial likelihood deviation, while the vertical solid line represents its corresponding 95% confidence interval. (B) The coefficient values at varying levels of penalty. Each curve represents an lncRNA. (C) The immune-related ceRNA network. The yellow quadrilateral represents lncRNA, the red triangle represents miRNA, while the blue circle represents genes. The degree of connection of the nodes is indicated by the size of the shape and the thickness of the edge. (D) Venn diagram of endometrial SAB genes (ESABGs) and DEGs. (E) Venn diagram of ESABGs and immune-related differentially expressed genes (IRDEGs). (F) The bar chart shows that EASG has a larger proportion in the IRDEG. (G) The immune-related endometrial SAB ceRNA network. The yellow quadrilateral represents lncRNA, the red triangle represents miRNA, while the blue circle represents genes. The degree of connection of the nodes is indicated by the size of the shape and the thickness of the edge. (H) Relative expression of the DELs and several DEGs in the ceRNA network. Full article ">Figure 7
Assessment of lncRNA and miRNA conservation. (A) Schematic diagram of the 45,451,130–45,469,626 bp genome annotation of pig chromosome 18, depicted with the gene loci of HOXA3 and the identified lncRNA TCONS_00167675, which is highlighted by the red boxes. (B) Alignment of ssc-miR-9824-5p with miRNAs of different species in the seed region. (C) Relative expression levels of TCONS_00161675 and HOXA3. Full article ">

20 pages, 4162 KiB

Open AccessArticle

Putative Cooperative ATP–DnaA Binding to Double-Stranded DnaA Box and Single-Stranded DnaA-Trio Motif upon Helicobacter pylori Replication Initiation Complex Assembly

by Pawel Jaworski, Dorota Zyla-Uklejewicz, Malgorzata Nowaczyk-Cieszewska, Rafal Donczew, Thorsten Mielke, Christoph Weigel and Anna Zawilak-Pawlik

Int. J. Mol. Sci. 2021, 22(12), 6643; https://doi.org/10.3390/ijms22126643 - 21 Jun 2021

Cited by 7 | Viewed by 3048

Abstract

oriC is a region of the bacterial chromosome at which the initiator protein DnaA interacts with specific sequences, leading to DNA unwinding and the initiation of chromosome replication. The general architecture of oriCs is universal; however, the structure of oriC and the [...] Read more.

oriC is a region of the bacterial chromosome at which the initiator protein DnaA interacts with specific sequences, leading to DNA unwinding and the initiation of chromosome replication. The general architecture of oriCs is universal; however, the structure of oriC and the mode of orisome assembly differ in distantly related bacteria. In this work, we characterized oriC of Helicobacter pylori, which consists of two DnaA box clusters and a DNA unwinding element (DUE); the latter can be subdivided into a GC-rich region, a DnaA-trio and an AT-rich region. We show that the DnaA-trio submodule is crucial for DNA unwinding, possibly because it enables proper DnaA oligomerization on ssDNA. However, we also observed the reverse effect: DNA unwinding, enabling subsequent DnaA–ssDNA oligomer formation—stabilized DnaA binding to box ts1. This suggests the interplay between DnaA binding to ssDNA and dsDNA upon DNA unwinding. Further investigation of the ts1 DnaA box revealed that this box, together with the newly identified c-ATP DnaA box in oriC1, constitute a new class of ATP–DnaA boxes. Indeed, in vitro ATP–DnaA unwinds H. pylori oriC more efficiently than ADP–DnaA. Our results expand the understanding of H. pylori orisome formation, indicating another regulatory pathway of H. pylori orisome assembly. Full article

(This article belongs to the Section Molecular Biology)

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18 pages, 1540 KiB

Open AccessReview

Targeting Mitochondria in Diabetes

by Nina Krako Jakovljevic, Kasja Pavlovic, Aleksandra Jotic, Katarina Lalic, Milica Stoiljkovic, Ljiljana Lukic, Tanja Milicic, Marija Macesic, Jelena Stanarcic Gajovic and Nebojsa M. Lalic

Int. J. Mol. Sci. 2021, 22(12), 6642; https://doi.org/10.3390/ijms22126642 - 21 Jun 2021

Cited by 64 | Viewed by 9301

Abstract

Type 2 diabetes (T2D), one of the most prevalent noncommunicable diseases, is often preceded by insulin resistance (IR), which underlies the inability of tissues to respond to insulin and leads to disturbed metabolic homeostasis. Mitochondria, as a central player in the cellular energy [...] Read more.

Type 2 diabetes (T2D), one of the most prevalent noncommunicable diseases, is often preceded by insulin resistance (IR), which underlies the inability of tissues to respond to insulin and leads to disturbed metabolic homeostasis. Mitochondria, as a central player in the cellular energy metabolism, are involved in the mechanisms of IR and T2D. Mitochondrial function is affected by insulin resistance in different tissues, among which skeletal muscle and liver have the highest impact on whole-body glucose homeostasis. This review focuses on human studies that assess mitochondrial function in liver, muscle and blood cells in the context of T2D. Furthermore, different interventions targeting mitochondria in IR and T2D are listed, with a selection of studies using respirometry as a measure of mitochondrial function, for better data comparison. Altogether, mitochondrial respiratory capacity appears to be a metabolic indicator since it decreases as the disease progresses but increases after lifestyle (exercise) and pharmacological interventions, together with the improvement in metabolic health. Finally, novel therapeutics developed to target mitochondria have potential for a more integrative therapeutic approach, treating both causative and secondary defects of diabetes. Full article

(This article belongs to the Special Issue Targeting Mitochondria in Metabolic Diseases)

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Cellular mechanisms underlying exercise as lifestyle intervention in T2D. Exercise increases insulin sensitivity in T2D by affecting energy metabolism through induction of mitochormesis, stimulation of mitochondrial turnover and biogenesis, increase in Ca2+ concentration, AMP/ATP and NAD+/NADH ratios and increase in respiration: ROUTINE, LEAK, OXPHOS and ET capacity. Symbol: ↑ = increase. Full article ">Figure 2
Potential mitochondria targeting agents that might improve insulin sensitivity through modulation of mitochondrial function. They are grouped based on the strategy of their pharmacological actions, which implies potential molecular mechanisms: NBMs (NAD+ boosting molecules), mitochondrial membrane properties modulators, STACs (Sirt1-activating compounds), OXPHOS modulators, AMPK activators, PPAR agonists, antioxidants (ROS scavenger), MCP (mitochondrial pyruvate carrier) inhibitors, CI (respiratory complex I) inhibitors, mPTP (mitochondrial permeability transition pore) inhibitors, CoQ10 (coenzyme Q10) analogues, mitochondrial-associated ER membranes (MAM) modulators and novel drugs to be designed. Symbols: ? = unknown drug—to be designed; ↑ = increase. Full article ">Figure 3
Mitochondria as an effector target of main diabetogenic factors such as obesity, aging and sedentary habits, which all cause a decrease of respiratory capacity, while the lifestyle and pharmacological interventions cause an increase of respiratory capacity and improvement of metabolic health. Full article ">

15 pages, 3882 KiB

Open AccessArticle

Mitochondrial Function Are Disturbed in the Presence of the Anticancer Drug, 3-Bromopyruvate

by Magdalena Cal, Irwin Matyjaszczyk, Karolina Filik, Rafał Ogórek, Young Ko and Stanisław Ułaszewski

Int. J. Mol. Sci. 2021, 22(12), 6640; https://doi.org/10.3390/ijms22126640 - 21 Jun 2021

Cited by 4 | Viewed by 3579

Abstract

3-bromopuryvate (3-BP) is a compound with unique antitumor activity. It has a selective action against tumor cells that exhibit the Warburg effect. It has been proven that the action of 3-BP is pleiotropic: it acts on proteins, glycolytic enzymes, reduces the amount of [...] Read more.

3-bromopuryvate (3-BP) is a compound with unique antitumor activity. It has a selective action against tumor cells that exhibit the Warburg effect. It has been proven that the action of 3-BP is pleiotropic: it acts on proteins, glycolytic enzymes, reduces the amount of ATP, induces the formation of ROS (reactive oxygen species), and induces nuclear DNA damage. Mitochondria are important organelles for the proper functioning of the cell. The production of cellular energy (ATP), the proper functioning of the respiratory chain, or participation in the production of amino acids are one of the many functions of mitochondria. Here, for the first time, we show on the yeast model that 3-BP acts in the eukaryotic cell also by influence on mitochondria and that agents inhibiting mitochondrial function can potentially be used in cancer therapy with 3-BP. We show that cells with functional mitochondria are more resistant to 3-BP than rho⁰ cells. Using an MTT assay (a colorimetric assay for assessing cell metabolic activity), we demonstrated that 3-BP decreased mitochondrial activity in yeast in a dose-dependent manner. 3-BP induces mitochondrial-dependent ROS generation which results in ∆sod2, ∆por1, or ∆gpx1 mutant sensitivity to 3-BP. Probably due to ROS mtDNA lesions rise during 3-BP treatment. Our findings may have a significant impact on the therapy with 3-BP. Full article

(This article belongs to the Special Issue Advances in Molecular Activity of Potential Drugs)

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3-BP causes cell death in yeast W303-1A (WT) and rho0 strain. Logarithmically growing W303-1A (WT) and rho0 cells were treated for 4 h with different 3-BP concentrations, incubated with PI, and viewed under a fluorescence microscope. Percent of PI-positive cells was calculated. * p ≤ 0.05. Full article ">Figure 2
rho0 mutants exhibit increased sensitivity to 3-BP. Spot tests were performed to test the sensitivity of rho0 and WT strain to 3-BP. Serial dilutions of strains were spotted on SD medium plates with different 3-BP concentrations and incubated for 2 days at 30 °C. Full article ">Figure 3
3-BP leads to inhibition of mitochondrial activity in yeast. Logarithmically growing W303-1A (WT) cells were treated for 2 h with different 3-BP concentrations and collected. OD600 was adjusted to 0.5 in PBS and cells were incubated for 4 h in presence of 0.5 mg/mL MTT. * p ≤ 0.05; ** p ≤ 0.01. Full article ">Figure 4
3-BP induces generation of superoxide in mitochondria. Mitochondrial superoxide level was measured with a MitoSOX fluorescent probe. WT cells were treated with different 3-BP concentrations for 4 h and loaded with MitoSOX Red, signal was detected under a fluorescence microscope. The percentage of cells with a mitochondrial signal was calculated. Yeast cells that exhibit fluorescence from the whole-cell represent dead cells and were not taken into account. ** p ≤ 0.01. Full article ">Figure 5
3-BP causes an increase in mtDNA lesions detected in the QPCR assay. Logarithmically growing WT cells were treated with indicated 3-BP concentrations and 0.1% MMS for 5 h and DNA was extracted from cells. DNA concentrations were adjusted and PCR was run to amplify 6.9 kb fragment of mitochondrial COX1 gene. dsDNA content was measured with QuantiFluor (Promega). PCR products were visualized with agarose gel electrophoresis. * p ≤ 0.05; ** p ≤ 0.01; *** p ≤ 0.001. Full article ">Figure 6
3-BP works synergistically with agents inducing oxidative stress and inhibiting mitochondrial ETC (electron transport chain). Spot tests were performed to test the sensitivity of wild type (BY4743, W303-1A), rho0, Δsod2 to 3-BP in combination with Antimycin-A and H2O2. Serial dilutions of strains were spotted on SD medium plates with different concentrations of compounds and incubated for 2 days at 30 °C. Full article ">Figure 7
Deletion mutants strains of mtDNA maintenance, repair, and ROS protection genes exhibit increased sensitivity to 3-BP. Serial dilutions of strains were spotted on SD medium plates with different 3-BP concentrations and incubated for 2 days at 30 °C. Full article ">Figure 8
Possible mechanisms of 3-BP’s killing actions to cells. After entering the cell through MCTs’ channels, 3-BP inhibits glycolytic enzymes (i.e., HK2, GAPDH) and mitochondrial oxidative phosphorylation pathway (i.e., complex II/SDH). Additionally, 3-BP leads to a reduction in the amount of glutathione while increasing the level of ROS. By disrupting the mitochondrial electron transport chain, 3-BP leads to the generation of mitochondrial-dependent ROS, which results in mtDNA damage. Excess ROS may potentially induce damage to genomic DNA. Full article ">

11 pages, 2496 KiB

Open AccessArticle

Virtual Evolution of HVEM Segment for Checkpoint Inhibitor Discovery

by Mingjia Yu, Huimin Zhao, Yuhui Miao, Shi-Zhong Luo and Song Xue

Int. J. Mol. Sci. 2021, 22(12), 6638; https://doi.org/10.3390/ijms22126638 - 21 Jun 2021

Cited by 7 | Viewed by 3200

Abstract

Immune therapy has emerged as an effective treatment against cancers. Inspired by the PD-1/PD-L1 antibodies, which have achieved great success in clinical, other immune checkpoint proteins have drawn increasing attention in cancer research. B and T lymphocyte attenuator (BTLA) and herpes virus entry [...] Read more.

Immune therapy has emerged as an effective treatment against cancers. Inspired by the PD-1/PD-L1 antibodies, which have achieved great success in clinical, other immune checkpoint proteins have drawn increasing attention in cancer research. B and T lymphocyte attenuator (BTLA) and herpes virus entry mediator (HVEM) are potential targets for drug development. The co-crystal structure of BTLA/HVEM have revealed that HVEM (26–38) fragment is the core sequence which directly involved on the interface. Herein, we conducted virtual evolution with this sequence by using saturation mutagenesis in silico and mutants with lower binding energy were selected. Wet-lab experiments confirmed that several of them possessed higher affinity with BTLA. Based on the best mutant of the core sequence, extended peptides with better efficacy were obtained. Furthermore, the mechanism of the effects of mutations was revealed by computational analysis. The mutated peptide discovered here can be a potent inhibitor to block BTLA/HVEM interaction and its mechanism may extend people’s view on inhibitor discovery for the checkpoint pair. Full article

(This article belongs to the Special Issue Structure, Function and Evolution of Protein Domains)

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18 pages, 1084 KiB

Open AccessReview

Novel Applications of NSAIDs: Insight and Future Perspectives in Cardiovascular, Neurodegenerative, Diabetes and Cancer Disease Therapy

by Edmundas Kaduševičius

Int. J. Mol. Sci. 2021, 22(12), 6637; https://doi.org/10.3390/ijms22126637 - 21 Jun 2021

Cited by 27 | Viewed by 7891

Abstract

Once it became clear that inflammation takes place in the modulation of different degenerative disease including neurodegenerative, cardiovascular, diabetes and cancer the researchers has started intensive programs evaluating potential role of non-steroidal anti-inflammatory drugs (NSAIDs) in the prevention or therapy of these diseases. [...] Read more.

Once it became clear that inflammation takes place in the modulation of different degenerative disease including neurodegenerative, cardiovascular, diabetes and cancer the researchers has started intensive programs evaluating potential role of non-steroidal anti-inflammatory drugs (NSAIDs) in the prevention or therapy of these diseases. This review discusses the novel mechanism of action of NSAIDs and its potential use in the pharmacotherapy of neurodegenerative, cardiovascular, diabetes and cancer diseases. Many different molecular and cellular factors which are not yet fully understood play an important role in the pathogenesis of inflammation, axonal damage, demyelination, atherosclerosis, carcinogenesis thus further NSAID studies for a new potential indications based on precise pharmacotherapy model are warranted since NSAIDs are a heterogeneous group of medicines with relative different pharmacokinetics and pharmacodynamics profiles. Hopefully the new data from studies will fill in the gap between experimental and clinical results and translate our knowledge into successful disease therapy. Full article

(This article belongs to the Special Issue Molecular Mechanism(s) of Non-steroidal Anti-inflammatory Drugs in the Prevention of Metabolic Diseases)

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17 pages, 2316 KiB

Open AccessReview

Natural Phytochemicals Derived from Gymnosperms in the Prevention and Treatment of Cancers

by Tayyebeh Ghaffari, Joo-Hyun Hong, Solmaz Asnaashari, Safar Farajnia, Abbas Delazar, Hamed Hamishehkar and Ki Hyun Kim

Int. J. Mol. Sci. 2021, 22(12), 6636; https://doi.org/10.3390/ijms22126636 - 21 Jun 2021

Cited by 14 | Viewed by 5536

Abstract

The incidence of various types of cancer is increasing globally. To reduce the critical side effects of cancer chemotherapy, naturally derived compounds have been considered for cancer treatment. Gymnosperms are a group of plants found worldwide that have traditionally been used for therapeutic [...] Read more.

The incidence of various types of cancer is increasing globally. To reduce the critical side effects of cancer chemotherapy, naturally derived compounds have been considered for cancer treatment. Gymnosperms are a group of plants found worldwide that have traditionally been used for therapeutic applications. Paclitaxel is a commercially available anticancer drug derived from gymnosperms. Other natural compounds with anticancer activities, such as pinostrobin and pinocembrin, are extracted from pine heartwood, and pycnogenol and enzogenol from pine bark. Gymnosperms have great potential for further study for the discovery of new anticancer compounds. This review aims to provide a rational understanding and the latest developments in potential anticancer compounds derived from gymnosperms. Full article

(This article belongs to the Special Issue Phytochemicals from Aromatic and Medicinal Plants: From Identification to Biomedical Applications)

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Chemical structures of the commercially available products displayed in <a href="#ijms-22-06636-t001" class="html-table">Table 1</a>. Full article ">Figure 2
Possible mechanism of paclitaxel action. Paclitaxel targets microtubules and inhibits the depolymerization of microtubules by binding to β-tubulin and leading to cell death. Solute carrier organic anion transporter family member 1B3, which is expressed in various tumors, is the most effective influx transporter for paclitaxel. Paclitaxel induces apoptosis via reactive oxygen species production as well as p21, B-cell lymphoma-2 associated X protein, and caspase overexpression and also activates the Toll-like receptor 4/nuclear factor kappa B pathway. (adopted with modification from [<a href="#B12-ijms-22-06636" class="html-bibr">12</a>]). Full article ">Figure 3
Mechanism of pycnogenol anticancer and antioxidant action. Pycnogenol can inhibit PKC and telomerase in cancer cells for life-span reduction. Furthermore, by reducing NFκB activation, VCAM-1 and ICAM-1 can prevent cancer. Pycnogenol has anti-diabetic and cardioprotective effects through increasing nitric oxide levels and reducing lipid peroxidation. Full article ">Figure 4
Mechanism of pinocembrin induction of apoptosis in cancer cells. In the intrinsic pathway, the expression of the pro-apoptotic proteins B-cell lymphoma-2 (Bcl-2) associated X protein, Bcl-2 homologous antagonist/killer, and Bcl-2-like protein 11 increases and that of the anti-apoptotic proteins Bcl-2 and Bcl-extra-large decreases. Cytochrome c translocates from the mitochondria to the cytosol, leading to apoptosis. In the extrinsic pathway, pinocembrin leads to apoptosis via the Fas-associated protein death domain/caspase-8/caspase-3 signaling pathway. Full article ">Figure 5
Mechanism of action of leelamine. Leelamine disrupts receptor tyrosine kinase signaling pathways, leading to a decrease in the phosphoinositide 3-kinase/protein kinase B, mitogen-activated protein kinase, and signal transducer and activator of transcription 3 signaling cascades, resulting in the reduction of B cell lymphoma (Bcl) 2 and Bcl-extra-large expression levels. Full article ">Figure 6
Mechanism of action of stilbenoids. Stilbenoids induces apoptosis through the caspase activation pathway; they also suppress Bcl-2 expression and apoptosome production. Stilbenoids induce autophagy in cancer cells in an hsp-70 dependent mechanism. These compounds suppress the NF-κB signaling pathway that plays an important role in inflammation. They also activate the Nrf2 antioxidant defense system (adopted with modification from [<a href="#B107-ijms-22-06636" class="html-bibr">107</a>]). Full article ">

11 pages, 525 KiB

Open AccessReview

Contribution of K2P Potassium Channels to Cardiac Physiology and Pathophysiology

by Salvador Herrera-Pérez, Ana Campos-Ríos, Lola Rueda-Ruzafa and José Antonio Lamas

Int. J. Mol. Sci. 2021, 22(12), 6635; https://doi.org/10.3390/ijms22126635 - 21 Jun 2021

Cited by 10 | Viewed by 4382

Abstract

Years before the first two-pore domain potassium channel (K2P) was cloned, certain ion channels had already been demonstrated to be present in the heart with characteristics and properties usually attributed to the TREK channels (a subfamily of K2P channels). K2P channels were later [...] Read more.

Years before the first two-pore domain potassium channel (K2P) was cloned, certain ion channels had already been demonstrated to be present in the heart with characteristics and properties usually attributed to the TREK channels (a subfamily of K2P channels). K2P channels were later detected in cardiac tissue by RT-PCR, although the distribution of the different K2P subfamilies in the heart seems to depend on the species analyzed. In order to collect relevant information in this regard, we focus here on the TWIK, TASK and TREK cardiac channels, their putative roles in cardiac physiology and their implication in coronary pathologies. Most of the RNA expression data and electrophysiological recordings available to date support the presence of these different K2P subfamilies in distinct cardiac cells. Likewise, we show how these channels may be involved in certain pathologies, such as atrial fibrillation, long QT syndrome and Brugada syndrome. Full article

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

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13 pages, 691 KiB

Open AccessReview

Mitochondrial DNA Copy Number and Developmental Origins of Health and Disease (DOHaD)

by Hisanori Fukunaga

Int. J. Mol. Sci. 2021, 22(12), 6634; https://doi.org/10.3390/ijms22126634 - 21 Jun 2021

Cited by 21 | Viewed by 6568

Abstract

Mitochondrial dysfunction is known to contribute to mitochondrial diseases, as well as to a variety of aging-based pathologies. Mitochondria have their own genomes (mitochondrial DNA (mtDNA)) and the abnormalities, such as point mutations, deletions, and copy number variations, are involved in mitochondrial dysfunction. [...] Read more.

Mitochondrial dysfunction is known to contribute to mitochondrial diseases, as well as to a variety of aging-based pathologies. Mitochondria have their own genomes (mitochondrial DNA (mtDNA)) and the abnormalities, such as point mutations, deletions, and copy number variations, are involved in mitochondrial dysfunction. In recent years, several epidemiological studies and animal experiments have supported the Developmental Origin of Health and Disease (DOHaD) theory, which states that the environment during fetal life influences the predisposition to disease and the risk of morbidity in adulthood. Mitochondria play a central role in energy production, as well as in various cellular functions, such as apoptosis, lipid metabolism, and calcium metabolism. In terms of the DOHaD theory, mtDNA copy number may be a mediator of health and disease. This paper summarizes the results of recent epidemiological studies on the relationship between environmental factors and mtDNA copy number during pregnancy from the perspective of DOHaD theory. The results of these studies suggest a hypothesis that mtDNA copy number may reflect environmental influences during fetal life and possibly serve as a surrogate marker of health risks in adulthood. Full article

(This article belongs to the Special Issue Mitochondrial DNA and RNA)

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12 pages, 1866 KiB

Open AccessArticle

Preconceptional Immunization Can Modulate Offspring Intrathymic IL-17-Producing γδT Cells with Epigenetic Implications Mediated by microRNAs

by Thamires Rodrigues de-Sousa, Rodrigo Pessôa, Andrezza Nascimento, Beatriz Oliveira Fagundes, Fábio da Ressureição Sgnotto, Alberto José da Silva Duarte, Sabri Saeed Sanabani and Jefferson Russo Victor

Int. J. Mol. Sci. 2021, 22(12), 6633; https://doi.org/10.3390/ijms22126633 - 21 Jun 2021

Cited by 1 | Viewed by 2684

Abstract

The mechanisms through which maternal immunization can modulate offspring thymic maturation of lymphocytes are not fully understood. Here, we aimed to evaluate whether maternal OVA-immunization can inhibit the maturation of IL-17-producing γδT cells in offspring thymus, and if this mechanism has epigenetic implications [...] Read more.

The mechanisms through which maternal immunization can modulate offspring thymic maturation of lymphocytes are not fully understood. Here, we aimed to evaluate whether maternal OVA-immunization can inhibit the maturation of IL-17-producing γδT cells in offspring thymus, and if this mechanism has epigenetic implications mediated by microRNAs (miRNAs) expression. Wild-type (WT) C57BL/6 females were immunized with OVA in Alum or Alum alone and were mated with normal WT males. Evaluating their offspring thymus at 3 or 20 days old (d.o.), we observed that maternal OVA immunization could inhibit the thymic frequency of offspring CD27- and IL-17⁺ γδT cells at the neonatal and until 20 days old. Furthermore, we evaluated the expression of function-related γ and δ variable γδTCR chains (Vγ1, Vγ2, Vγ3, Vδ4, and Vδ6.3), observing that maternal OVA-immunization inhibits Vγ2 chains expression. The small RNAs (sRNAs), particularly miRNAs, and messenger RNAs (mRNA) expression profiles by pools of thymus tissue samples (from 9 to 11 mice) from offspring OVA-immunized or Alum-immunized mothers were analyzed via Illumina sequencing platform and bioinformatics approaches. Using a fold change >4, our results showed that seven miRNAs (mmu-miR-126a-3p, 101a-3p, 744-3p,142-5p, 15a-5p, 532-5p, and 98-5p) were differentially expressed between both groups. Ten target genes were predicted to interact with the seven selected miRNAs. There were no enriched categories of gene ontology functional annotation and pathway enrichment analysis for the target genes. Interestingly, four of the identified miRNAs (mmu-miR-15a, mmu-miR-101 mmu-miR-126, and mmu-miR-142) are related to IL-17 production. Our data is of significance because we demonstrate that maternal immunization can modulate offspring thymic maturation of IL-17-producing γδT cells possibly by an epigenetic mechanism mediated by miRNAs. Full article

(This article belongs to the Section Biochemistry)

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Figure 1
Induction of offspring allergy tolerance mediated by maternal immunization with OVA. Offspring from OVA-immunized (n = 10) or Alum-immunized (n = 11) mothers were immunized with OVA in the neonatal period. At 20 d.o., offspring total IgE was determined by ELISA (a). These groups were subjected to an allergic lung inflammation protocol with OVA, and differential cell counts in BAL (b) were evaluated by flow cytometry. The percentage of infiltrated lymphocytes, the frequency of γδT cells, and the frequency of CD27- γδT cells was evaluated in the dissociated lung tissue (c) by flow cytometry. The results are illustrated with violin plot (truncated) representing median (bold line) and the quartiles (thin lines). * p ≤ 0.05 compared to Alum-immunized offspring. Full article ">Figure 2
Inhibition of offspring thymic maturation of IL-17-producing and Vγ2+ γδT cells mediated by maternal immunization with OVA. Offspring from OVA-immunized (n = 9) or Alum-immunized (n = 10) mothers were evaluated. Thymic frequency of total and IL-17-producing (IL-17+) γδT cells were evaluated by flow cytometry at 3 (a) and 20 (b) d.o. offspring. Additionally, thymic frequency of Vγ1, Vγ2, Vγ3, Vδ4, and Vδ6.3 γδT cells was evaluated at 3 (c) d.o. offspring by flow cytometry. The results are illustrated with violin plot (truncated) representing median (bold line) and the quartiles (thin lines). *p ≤ 0.05 compared to Alum-immunized offspring. Full article ">Figure 3
miRNAs that were downregulated by maternal OVA immunization. The thymus of offspring from OVA-immunized (n = 10) or Alum-immunized (n = 11) mothers was evaluated at three days old. Unsupervised hierarchical clustering demonstrating 52 differentially expressed mature mmu-miRs between offspring OVA-immunized and Alum-immunized mothers. The mmu-miRs clustering tree is displayed to the right, forming two major clusters. The color scale at the bottom indicates the fold change expression levels of mature mmu-miRs across in both samples: red color indicates overexpression and blue underexpression. Full article ">Figure 4
miRNAs that were substantially modulated between groups. The thymus of offspring from OVA-immunized (n = 10) or Alum-immunized (n = 11) mothers was evaluated at three days old. The dots showed the seven dysregulated miRNAs between offspring from Alum and OVA-immunized mothers. The fold change in these miRNAs was set at cut-off ≥4. Full article ">

13 pages, 970 KiB

Open AccessReview

The Role of Neuropeptide B and Its Receptors in Controlling Appetite, Metabolism, and Energy Homeostasis

by Tatiana Wojciechowicz, Maria Billert, Mariami Jasaszwili, Mathias Z. Strowski, Krzysztof W. Nowak and Marek Skrzypski

Int. J. Mol. Sci. 2021, 22(12), 6632; https://doi.org/10.3390/ijms22126632 - 21 Jun 2021

Cited by 6 | Viewed by 3336

Abstract

Neuropeptide B (NPB) is a peptide hormone that was initially described in 2002. In humans, the biological effects of NPB depend on the activation of two G protein-coupled receptors, NPBWR1 (GPR7) and NPBWR2 (GPR8), and, in rodents, NPBWR1. NPB and its receptors are [...] Read more.

Neuropeptide B (NPB) is a peptide hormone that was initially described in 2002. In humans, the biological effects of NPB depend on the activation of two G protein-coupled receptors, NPBWR1 (GPR7) and NPBWR2 (GPR8), and, in rodents, NPBWR1. NPB and its receptors are expressed in the central nervous system (CNS) and in peripheral tissues. NPB is also present in the circulation. In the CNS, NPB modulates appetite, reproduction, pain, anxiety, and emotions. In the peripheral tissues, NPB controls secretion of adrenal hormones, pancreatic beta cells, and various functions of adipose tissue. Experimental downregulation of either NPB or NPBWR1 leads to adiposity. Here, we review the literature with regard to NPB-dependent control of metabolism and energy homeostasis. Full article

(This article belongs to the Special Issue Neuropeptides in Food Intake Regulation)

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15 pages, 2280 KiB

Open AccessArticle

D-Amino Acid-Containing Lipopeptides Derived from the Lead Peptide BP100 with Activity against Plant Pathogens

by Àngel Oliveras, Luís Moll, Gerard Riesco-Llach, Arnau Tolosa-Canudas, Sergio Gil-Caballero, Esther Badosa, Anna Bonaterra, Emilio Montesinos, Marta Planas and Lidia Feliu

Int. J. Mol. Sci. 2021, 22(12), 6631; https://doi.org/10.3390/ijms22126631 - 21 Jun 2021

Cited by 11 | Viewed by 3125

Abstract

From a previous collection of lipopeptides derived from BP100, we selected 18 sequences in order to improve their biological profile. In particular, analogues containing a D-amino acid at position 4 were designed, prepared, and tested against plant pathogenic bacteria and fungi. The [...] Read more.

From a previous collection of lipopeptides derived from BP100, we selected 18 sequences in order to improve their biological profile. In particular, analogues containing a D-amino acid at position 4 were designed, prepared, and tested against plant pathogenic bacteria and fungi. The biological activity of these sequences was compared with that of the corresponding parent lipopeptides with all L-amino acids. In addition, the influence of the length of the hydrophobic chain on the biological activity was evaluated. Interestingly, the incorporation of a D-amino acid into lipopeptides bearing a butanoyl or a hexanoyl chain led to less hemolytic sequences and, in general, that were as active or more active than the corresponding all L-lipopeptides. The best lipopeptides were BP475 and BP485, both incorporating a D-Phe at position 4 and a butanoyl group, with MIC values between 0.8 and 6.2 µM, low hemolysis (0 and 24% at 250 µM, respectively), and low phytotoxicity. Characterization by NMR of the secondary structure of BP475 revealed that the D-Phe at position 4 disrupts the α-helix and that residues 6 to 10 are able to fold in an α-helix. This secondary structure would be responsible for the high antimicrobial activity and low hemolysis of this lipopeptide. Full article

(This article belongs to the Special Issue Design and Synthesis of Peptides: Impact on Current Biomedicine, Biotechnology, and Chemical Biology)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
Antimicrobial activity of lipopeptides against the bacteria E. amylovora (Ea), P. syringae pv. syringae (Pss), P. syringae pv. actinidiae (Psa), X. fragariae (Xf), X. arboricola pv. pruni (Xap) and X. axonopodis pv. vesicatoria (Xav), and the fungi P. expansum (Pe) and F. oxysporum (Fo). The type of acyl group is indicated below the lipopeptides. Antimicrobial activity is given as the minimal concentration that inhibits growth (MIC). The MIC axis is in logarithmic scale, and for each sequence, the lowest values of the MIC range is represented. Data can be found in <a href="#app1-ijms-22-06631" class="html-app">Table S1 (Supplementary Materials</a>). Full article ">Figure 2
Overlay of HN-HN and HN-Hα TOCSY (red) and NOESY (blue) correlations for (a) BP389 and (b) BP475 in phosphate buffer; (c) BP389 and (d) BP475 in phosphate buffer with 30% CF3CD2OD. Full article ">Figure 3
Secondary structure adopted by each peptide. Numbers indicate the position of the amino acids. The red curve represents an α-helix, while the black line stands for a random coil region. Full article ">Figure 4
Antimicrobial activity of lipopeptides incorporating all L-amino acids or a D-amino acid against E. amylovora (Ea), P. syringae pv. syringae (Pss), P. syringae pv. actinidiae (Psa), X. fragariae (Xf), X. arboricola pv. pruni (Xap) and X. axonopodis pv. vesicatoria (Xav), and the fungi P. expansum (Pe) and F. oxysporum (Fo). The x axis includes the code for each lipopeptide. The residue that can be a L- or a D-amino acid is indicated in italics. Antimicrobial activity is given as the minimal concentration that inhibits growth (MIC). The MIC axis is in logarithmic scale and for each sequence the lowest values of the MIC range is represented. Black symbols correspond to the activity of lipopeptides with a D-amino acid, white symbols to the activity of lipopeptides with all L-amino acids, and grey symbols indicate that both lipopeptides display the same activity. Data can be found in <a href="#app1-ijms-22-06631" class="html-app">Table S1 (Supplementary Materials</a>). Full article ">Figure 5
Hemolytic activity of the lipopeptides incorporating all L-amino acids or a D-amino acid. The x axis includes the code for each lipopeptide. The residue that can be an L- or a D-amino acid is indicated in italics. Hemolytic activity was measured at 250 µM and is expressed as a percentage compared to melittin as a standard. Black squares correspond to the hemolysis of lipopeptides with a D-amino acid, white squares to the hemolysis of lipopeptides with all L-amino acids, and grey squares indicate that both lipopeptides display the same hemolysis. Data can be found in <a href="#app1-ijms-22-06631" class="html-app">Table S2 (Supplementary Materials</a>). Full article ">Figure 6
Effect of the lipopeptides incorporating all L-amino acids or a D-amino acid on the size of the lesions in infiltrated tobacco leaves at 250 µM. This effect was compared to melittin. Vertical bars within each column indicate confidence interval at the mean. The x axis includes the code for each lipopeptide. The residue that can be a L- or a D-amino acid is indicated in italics. Black bars correspond to lipopeptides with a D-amino acid and white bars to lipopeptides with all L-amino acids. Data can be found in <a href="#app1-ijms-22-06631" class="html-app">Table S3 (Supplementary Materials</a>). Full article ">

28 pages, 2848 KiB

Open AccessStudy Protocol

Epitranscriptomics of Ischemic Heart Disease—The IHD-EPITRAN Study Design and Objectives

by Vilbert Sikorski, Pasi Karjalainen, Daria Blokhina, Kati Oksaharju, Jahangir Khan, Shintaro Katayama, Helena Rajala, Satu Suihko, Suvi Tuohinen, Kari Teittinen, Annu Nummi, Antti Nykänen, Arda Eskin, Christoffer Stark, Fausto Biancari, Jan Kiss, Jarmo Simpanen, Jussi Ropponen, Karl Lemström, Kimmo Savinainen, Maciej Lalowski, Markku Kaarne, Mikko Jormalainen, Outi Elomaa, Pertti Koivisto, Peter Raivio, Pia Bäckström, Sebastian Dahlbacka, Simo Syrjälä, Tiina Vainikka, Tommi Vähäsilta, Nurcan Tuncbag, Mati Karelson, Eero Mervaala, Tatu Juvonen, Mika Laine, Jari Laurikka, Antti Vento and Esko Kankuri Show full author list Hide full author list

Int. J. Mol. Sci. 2021, 22(12), 6630; https://doi.org/10.3390/ijms22126630 - 21 Jun 2021

Cited by 9 | Viewed by 7514

Abstract

Epitranscriptomic modifications in RNA can dramatically alter the way our genetic code is deciphered. Cells utilize these modifications not only to maintain physiological processes, but also to respond to extracellular cues and various stressors. Most often, adenosine residues in RNA are targeted, and [...] Read more.

Epitranscriptomic modifications in RNA can dramatically alter the way our genetic code is deciphered. Cells utilize these modifications not only to maintain physiological processes, but also to respond to extracellular cues and various stressors. Most often, adenosine residues in RNA are targeted, and result in modifications including methylation and deamination. Such modified residues as N-6-methyl-adenosine (m⁶A) and inosine, respectively, have been associated with cardiovascular diseases, and contribute to disease pathologies. The Ischemic Heart Disease Epitranscriptomics and Biomarkers (IHD-EPITRAN) study aims to provide a more comprehensive understanding to their nature and role in cardiovascular pathology. The study hypothesis is that pathological features of IHD are mirrored in the blood epitranscriptome. The IHD-EPITRAN study focuses on m⁶A and A-to-I modifications of RNA. Patients are recruited from four cohorts: (I) patients with IHD and myocardial infarction undergoing urgent revascularization; (II) patients with stable IHD undergoing coronary artery bypass grafting; (III) controls without coronary obstructions undergoing valve replacement due to aortic stenosis and (IV) controls with healthy coronaries verified by computed tomography. The abundance and distribution of m⁶A and A-to-I modifications in blood RNA are charted by quantitative and qualitative methods. Selected other modified nucleosides as well as IHD candidate protein and metabolic biomarkers are measured for reference. The results of the IHD-EPITRAN study can be expected to enable identification of epitranscriptomic IHD biomarker candidates and potential drug targets. Full article

(This article belongs to the Special Issue Coronary Syndromes – Advances in Diagnostics and Therapy)

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Figure 1
Overview of the RNA m6A modification and A-to-I RNA editing and their known writers, readers, and erasers. m6A modification and A-to-I editing occur in most RNA species. ADAD1-2, adenosine deaminase domain-containing protein 1-2; ADAR1-3, double-stranded RNA-specific adenosine deaminase 1-3; ADAT1-3, adenosine deaminases acting on tRNAs; ALKBH5, alkB homolog 5 RNA demethylase; A-to-I, adenosine-to-inosine RNA editing; circRNA, circular RNA; ENDOV, human endonuclease V; eIF3, eukaryotic initiation factor 3; EWSR1, Ewing sarcoma breakpoint region 1 protein; FMRP, fragile X retardation protein; FTO, fat mass and obesity associated protein; G3BP1, Ras GTPase-activating protein-binding protein 1; HAKAI, E3 ubiquitin-protein ligase Hakai; HNRNP-A2B1,-C,-G, heterogeneous nuclear ribonucleoprotein A2/B1 and C1/C2 and G; HuR, human antigen R; IGF2BP1-3; The insulin-like growth factor-2 mRNA-binding proteins 1, 2, and 3; LIN28A, Lin-28 homolog A; lncRNA, long non-coding RNA; METTL3,-14,-16, N6- adenosine-methyltransferase catalytic subunit/non-catalytic subunit/METTL16; METTL5, methyltransferase Like 5; mRNA, messenger RNA; miRNA, microRNA; Prcc2a, proline rich coiled-coil 2 A; RBM15, RNA binding motif protein 15; rRNA, ribosomal RNA; snoRNA, small nucleolar RNA; TRMT112, TRNA methyltransferase subunit 11-2; tRNA, transfer RNA; VIRMA, vir like m6A methyltransferase associated; WTAP, Wilm’s tumor associated protein; (YTH)DC1-2, YTH domain-containing protein 1 ja 2; (YTH)DF1-3, YTH N6-methyladenosine RNA binding protein 1-3; ZCCHC4, zinc finger CCHC-type containing 4; ZC3H13, zinc finger CCCH domain-containing protein 13; *, miRNAs can also derive from pre-mRNA introns. Full article ">Figure 2
IHD-EPITRAN hypotheses (A). Coronary plaques signal bone marrow residing HSCs to increase proliferation promoting the efflorescence of CH and extramedullary hematopoiesis (Ly-6Chigh monocytosis), which both seed epitranscriptomically distinct cells to the circulation. (B). Leukocytes and platelets patrolling in the proximity and inside the atherosclerotic plaques, ischemic myocardium, and stressed endothelium oscillate back and seed EVs to the circulation with detectable alterations in their m6A and A-to-I RNA signatures. (C). The ischemic myocardium prime patrolling leukocytes and secrete paracrine EVs encasing m6A and A-to-I modified RNA molecules, entering also to the circulation. A-to-I, adenosine-to-inosine; CH, clonal hematopoiesis; EV, extracellular vesicle; HSC, hematopoietic stem cell; Ly6C, lymphocyte antigen 6; m6A, N6-methyladenosine; RBCs, red blood cells; TCs, thrombocytes; WBCs, white blood cells. Full article ">Figure 3
Outline and sample collection in the IHD-EPITRAN study. The gray scale provides an arbitrary scale for disease severity across cohorts. STEMI, ST-elevation myocardial infarction; CABG, coronary artery bypass grafting; AVR, aortic valve replacement; CCTA, coronary computed tomography angiogram; ICA, invasive coronary angiography; RAA, right atrial appendage; IHD, ischemic heart disease. Full article ">Figure 4
Study samples with respective principal analysis methods of the IHD-EPITRAN study. CVD, cardiovascular disease; FISH, fluorescence in situ hybridization; IHC, immunohistochemistry; IHD, ischemic heart disease; meRIP seq, methylated RNA immunoprecipitation sequencing; MRM, multiple reaction monitoring; RAA, right atrial appendage; UHPLC-MS/MS; ultra-high-performance triple quadrupole liquid chromatography tandem mass spectrometry. Full article ">Figure 5
Principal study cohort comparisons in the IHD-EPITRAN study. Referred outcomes are listed in <a href="#ijms-22-06630-t003" class="html-table">Table 3</a> (A). Venn diagram-based illustration of the preferred four-partite approach, due to its highest degree of adjustments, to acquire inter-cohort comparison-based outcomes. (B). Three-partite comparison scheme to enable comparisons even in the possible case of delay in one cohort recruitment, which is also the case with (C) depicting pairwise comparisons with lest adjustments for inter-cohort outcomes. Intracohort outcomes are achieved via pairwise prospective comparisons. (D). Timeline for the prospective outcome comparisons. Long-term follow-up of the study cohorts I-IV could provide dimensions of detecting incident and IHD exacerbations (<a href="#sec2dot6-ijms-22-06630" class="html-sec">Section 2.6</a> and Discussion). Abbreviations: AVR, aortic valve replacement cohort III; AVS, aortic valve stenosis; CABG, coronary artery bypass grafting cohort II; CCTA, coronary computed tomography angiogram cohort I; CVD, cardiovascular disease; IHD, ischemic heart disease, MACCE, major adverse cardiovascular and cerebrovascular event; PCI, percutaneous coronary intervention; STEMI, ST-elevation myocardial infarction cohort I. Full article ">

14 pages, 1168 KiB

Open AccessReview

Skeletal System Biology and Smoke Damage: From Basic Science to Medical Clinic

by Umberto Tarantino, Ida Cariati, Chiara Greggi, Elena Gasbarra, Alberto Belluati, Luigi Ciolli, Giulio Maccauro, Alberto Momoli, Simone Ripanti, Francesco Falez and Maria Luisa Brandi

Int. J. Mol. Sci. 2021, 22(12), 6629; https://doi.org/10.3390/ijms22126629 - 21 Jun 2021

Cited by 28 | Viewed by 7705

Abstract

Cigarette smoking has a negative impact on the skeletal system, as it reduces bone mass and increases fracture risk through its direct or indirect effects on bone remodeling. Recent evidence demonstrates that smoking causes an imbalance in bone turnover, making bone vulnerable to [...] Read more.

Cigarette smoking has a negative impact on the skeletal system, as it reduces bone mass and increases fracture risk through its direct or indirect effects on bone remodeling. Recent evidence demonstrates that smoking causes an imbalance in bone turnover, making bone vulnerable to osteoporosis and fragility fractures. Moreover, cigarette smoking is known to have deleterious effects on fracture healing, as a positive correlation between the daily number of cigarettes smoked and years of exposure has been shown, even though the underlying mechanisms are not fully understood. It is also well known that smoking causes several medical/surgical complications responsible for longer hospital stays and a consequent increase in the consumption of resources. Smoking cessation is, therefore, highly advisable to prevent the onset of bone metabolic disease. However, even with cessation, some of the consequences appear to continue for decades afterwards. Based on this evidence, the aim of our review was to evaluate the impact of smoking on the skeletal system, especially on bone fractures, and to identify the pathophysiological mechanisms responsible for the impairment of fracture healing. Since smoking is a major public health concern, understanding the association between cigarette smoking and the occurrence of bone disease is necessary in order to identify potential new targets for intervention. Full article

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

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9 pages, 4916 KiB

Open AccessArticle

The Unusual Role of Pro in Cu(II) Binding by His₂-Cyclopentapeptide

by Aleksandra Pieniężna, Aleksandra Kotynia and Justyna Brasuń

Int. J. Mol. Sci. 2021, 22(12), 6628; https://doi.org/10.3390/ijms22126628 - 21 Jun 2021

Viewed by 2033

Abstract

In this paper, we present findings from studying the interaction of copper(II) ions with the His₂-cyclopentapeptide and the role of proline used for the purpose of potentiometric titration and UV-Vis, CD and EPR spectroscopic measurements. Experiments of two homodetic peptides differing [...] Read more.

In this paper, we present findings from studying the interaction of copper(II) ions with the His₂-cyclopentapeptide and the role of proline used for the purpose of potentiometric titration and UV-Vis, CD and EPR spectroscopic measurements. Experiments of two homodetic peptides differing by one amino acid residue were conducted for a ligand to metal ratio of 1:1 in the pH range 2.5–11.0. The presented studies reveal that peptides form only mononuclear complexes, and the CuH₂L complex appears in the system first (for both L1 and L2). Study results show that the presence of Pro influences the structure of formed complexes and their stabilities and has a strong impact on the efficiency of copper(II) coordination. Full article

(This article belongs to the Section Biochemistry)

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The species distribution curves for the system of L1−c(GlyHisProHisLys) (solid line) and L2−c(GlyHisGlyHisLys) (dashed line). Full article ">Figure 2
The UV-Vis spectra for the solution with an equimolar quantity of (a) L1 and Cu(II) ions and (b) L2 and Cu(II) ions, at pH between 2.5 and 11.0. (c) The comparison of the experimental spectra for L1 at pH 4.0 (black) and L2 at pH 5.5 (red) obtained by the subtraction of the Cu(H2O)62+ spectrum. The CD spectra for the solution with an equimolar quantity of (d) L1−c(GlyHisProHisLys) and (e) L2−c(GlyHisGlyHisLys) with Cu(II) ions at pH between 2.5 and 11.0. Full article ">Figure 3
The competition plot between L1−c(GlyHisProHisLys) and L2−c(GlyHisGlyHisLys) in the presence of Cu(II) ions under the equimolar conditions. Full article ">Scheme 1
Schematic structures of investigated pentacyclopeptides: (a) L1—c(GlyHisProHisLys) and (b) L2—c(GlyHisGlyHisLys). The hydrogen atoms were omitted for simplicity; carbon atoms are grey; nitrogen atoms are blue; oxygen atoms are red. Full article ">Scheme 2
The proposed binding modes of (a) CuH2L, (b) CuL, (c) CuH-1L, and (d) CuH-2L visualized for L1−c(GlyHisProHisLys) peptide prepared by Avogadro Version 1.2.0. Full article ">Scheme 3
The characteristic HXXH motif presence in the investigated peptide. Full article ">

12 pages, 550 KiB

Open AccessReview

The Evolving Role of Fetuin-A in Nonalcoholic Fatty Liver Disease: An Overview from Liver to the Heart

by Teoman Dogru, Ali Kirik, Hasan Gurel, Ali A. Rizvi, Manfredi Rizzo and Alper Sonmez

Int. J. Mol. Sci. 2021, 22(12), 6627; https://doi.org/10.3390/ijms22126627 - 21 Jun 2021

Cited by 22 | Viewed by 4612

Abstract

Nonalcoholic fatty liver disease (NAFLD) is strongly associated to the features of metabolic syndrome which can progress to cirrhosis, liver failure and hepatocellular carcinoma. However, the most common cause of mortality in people with NAFLD is not liver-related but stems from atherosclerotic cardiovascular [...] Read more.

Nonalcoholic fatty liver disease (NAFLD) is strongly associated to the features of metabolic syndrome which can progress to cirrhosis, liver failure and hepatocellular carcinoma. However, the most common cause of mortality in people with NAFLD is not liver-related but stems from atherosclerotic cardiovascular disease (CVD). The prevalence of NAFLD is on the rise, mainly as a consequence of its close association with two major worldwide epidemics, obesity and type 2 diabetes (T2D). The exact pathogenesis of NAFLD and especially the mechanisms leading to disease progression and CVD have not been completely elucidated. Human fetuin-A (alpha-2-Heremans Schmid glycoprotein), a glycoprotein produced by the liver and abundantly secreted into the circulation appears to play a role in insulin resistance, metabolic syndrome and inflammation. This review discusses the links between NAFLD and CVD by specifically focusing on fetuin-A’s function in the pathogenesis of NAFLD and atherosclerotic CVD. Full article

(This article belongs to the Special Issue Metabolic Syndrome: From Molecular Mechanisms to Novel Therapies)

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32 pages, 979 KiB

Open AccessReview

Functions of Matricellular Proteins in Dental Tissues and Their Emerging Roles in Orofacial Tissue Development, Maintenance, and Disease

by Georgia Nikoloudaki

Int. J. Mol. Sci. 2021, 22(12), 6626; https://doi.org/10.3390/ijms22126626 - 21 Jun 2021

Cited by 14 | Viewed by 4507

Abstract

Matricellular proteins (MCPs) are defined as extracellular matrix (ECM) associated proteins that are important regulators and integrators of microenvironmental signals, contributing to the dynamic nature of ECM signalling. There is a growing understanding of the role of matricellular proteins in cellular processes governing [...] Read more.

Matricellular proteins (MCPs) are defined as extracellular matrix (ECM) associated proteins that are important regulators and integrators of microenvironmental signals, contributing to the dynamic nature of ECM signalling. There is a growing understanding of the role of matricellular proteins in cellular processes governing tissue development as well as in disease pathogenesis. In this review, the expression and functions of different MP family members (periostin, CCNs, TSPs, SIBLINGs and others) are presented, specifically in relation to craniofacial development and the maintenance of orofacial tissues, including bone, gingiva, oral mucosa, palate and the dental pulp. As will be discussed, each MP family member has been shown to have non-redundant roles in development, tissue homeostasis, wound healing, pathology and tumorigenesis of orofacial and dental tissues. Full article

(This article belongs to the Special Issue Matricellular Proteins: Modifiers of Cell Behavior in Development, Disease & Tissue Remodeling)

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14 pages, 1269 KiB

Open AccessArticle

Placental Glucose Transporters and Response to Bisphenol A in Pregnancies from of Normal and Overweight Mothers

by Leonardo Ermini, Anna Maria Nuzzo, Francesca Ietta, Roberta Romagnoli, Laura Moretti, Bianca Masturzo, Luana Paulesu and Alessandro Rolfo

Int. J. Mol. Sci. 2021, 22(12), 6625; https://doi.org/10.3390/ijms22126625 - 21 Jun 2021

Cited by 10 | Viewed by 3090

Abstract

Bisphenol A (BPA) is a synthetic phenol extensively used in the manufacture of polycarbonate plastics and epoxy resins and a component of liquid and food storages. Among health disorders potentially attributed to BPA, the effects on metabolism have been especially studied. BPA represents [...] Read more.

Bisphenol A (BPA) is a synthetic phenol extensively used in the manufacture of polycarbonate plastics and epoxy resins and a component of liquid and food storages. Among health disorders potentially attributed to BPA, the effects on metabolism have been especially studied. BPA represents a hazard in prenatal life because of its presence in tissues and fluids during pregnancy. Our recent study in rats fed with BPA showed a placental increase in glucose type 1 transporter (GLUT-1), suggesting a higher uptake of glucose. However, the role of BPA on GLUT transporters in pregnant women with metabolic dysfunction has not yet been investigated. In this study, placental tissue from 26 overweight (OW) women and 32 age-matched normal weight (NW) pregnant women were examined for expression of GLUT1 and GLUT4. Placental explants from OW and NW mothers were exposed to BPA 1 nM and 1 μM and tested for GLUTs expression. The data showed a different response of placental explants to BPA in GLUT1 expression with an increase in NW mothers and a decrease in OW ones. GLUT4 expression was lower in the explants from OW than NW mothers, while no difference was showed between OW and NW in placental biopsies for any of the transporters. Full article

(This article belongs to the Special Issue Molecular Connection between the Endocrine System and Body Regulation)

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12 pages, 1889 KiB

Open AccessArticle

Molecular Pathomechanisms of Impaired Flow-Induced Constriction of Cerebral Arteries Following Traumatic Brain Injury: A Potential Impact on Cerebral Autoregulation

by Annamaria Szenasi, Krisztina Amrein, Endre Czeiter, Nikolett Szarka, Peter Toth and Akos Koller

Int. J. Mol. Sci. 2021, 22(12), 6624; https://doi.org/10.3390/ijms22126624 - 21 Jun 2021

Cited by 5 | Viewed by 3591

Abstract

(1) Background: Traumatic brain injury (TBI) frequently occurs worldwide, resulting in high morbidity and mortality. Here, we hypothesized that TBI impairs an autoregulatory mechanism, namely the flow-induced constriction of isolated rat middle cerebral arteries (MCAs). (2) Methods: TBI was induced in anaesthetized rats [...] Read more.

(1) Background: Traumatic brain injury (TBI) frequently occurs worldwide, resulting in high morbidity and mortality. Here, we hypothesized that TBI impairs an autoregulatory mechanism, namely the flow-induced constriction of isolated rat middle cerebral arteries (MCAs). (2) Methods: TBI was induced in anaesthetized rats by weight drop model, and then MCAs were isolated and transferred into a pressure-flow chamber. The internal diameter was measured by a video-microscopy. (3) Results: In MCAs from intact rats, increases in flow and pressure + flow elicited constrictions (−26 ± 1.9 µm and −52 ± 2.8 µm, p < 0.05), which were significantly reduced after TBI or in the presence of thromboxane-prostanoid (TP receptor) antagonist SQ 29,548. Flow-induced constrictions were significantly reduced by HET0016, inhibitor of cytochrome P450 4A (CYP450 4A). Arachidonic acid, (AA, 10⁻⁷ M), and CYP-450 4A metabolite 20-hydroxyeicosatetraenoic acid (20-HETE) elicited constrictions of intact MCA (−26 ± 2.3% and −31 ± 3.6%), which were significantly reduced after TBI (to 11 ± 1.3% and −16 ±2.5%). The TP receptor agonist U46619 (10⁻⁷ M) elicited substantial constrictions of MCA from intact rats (−21 ± 3.3%), which were also significantly reduced, after TBI (to −16 ± 2.4%). (4) Conclusions: Flow-induced constrictor response of MCA is impaired by traumatic brain injury, likely due to the reduced ability of cytochrome P450 4A to convert arachidonic acid to constrictor prostaglandins and the mitigated sensitivity of thromboxane-prostanoid receptors. Full article

(This article belongs to the Special Issue Molecular Vascular Physiology)

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Figure 1
Changes in diameter of isolated middle cerebral arteries (MCAs) in response to step increases in intraluminal, flow (Δ0, Δ10, Δ20, Δ30, Δ40 mmHg between inflow and outflow cannulas) from intact rats and from rats after traumatic brain injury (TBI) in the absence and presence of SQ 29,548 (10−6 mol/L) an inhibitor of thromboxane A2 receptor (TP). Asterisks indicate significant differences * p < 0.05 vs. Intact flow and Intact flow with SQ 29,548 (n = 16, n = 8 in each group). Full article ">Figure 2
Shows the pressure (P)- or flow (F)-induced decreases in diameter alone, or the additive effect of pressure + flow on the diameter of MCA from intact rats. Additionally, <a href="#ijms-22-06624-f002" class="html-fig">Figure 2</a> shows that traumatic brain injury (TBI) significantly reduced the pressure (P)-, flow (F)-, and thus combined pressure + flow (P+F)-induced constrictions of MCAs (* indicates significant changes from Intact, # from P alone and F alone, and & from P+F (n = 24, data are mean ± SEM, p < 0.05) Moreover, this figure shows that HET0016 (10−6 mol/L), an inhibitor of cytochrome P450 4A (CYP450 4A), inhibited substantially and significantly the constriction induced by pressure + flow (n = 6 in each group). Full article ">Figure 3
In middle cerebral arteries (MCAs) isolated from intact rats, lower concentration of arachidonic acid (AA), after initial dilations, (left panel), elicited constrictions (right panel), whereas higher concentration of AA elicited only constriction. After traumatic brain injury (TBI), AA-induced responses were significantly reduced. Data are mean ± SEM of normalized diameter %. (*, **, # indicate p < 0.05). Full article ">Figure 4
This figure shows the mRNA expressions of the cytochrome isoforms Cyp4a1 and Cyp4a3 in middle cerebral arteries (MCAs) of INTACT and TBI rats, which were substantially reduced after TBI (n = 6 in each group). Full article ">Figure 5
Changes in diameter of isolated middle cerebral arteries (MCAs) in response to 20-hydroxyeicosatetraenoic acid (20-HETE, 10−7 mol/L) metabolite of cytochrome P450 4A enzyme (CYP450 4A) and U46619 (10−7 mol/L and 10−6 mol/L a stable agonist of TP receptors, intact and after traumatic brain injury (TBI). Data are mean ± SEM. Asterisks indicate significant differences (* p < 0.05 from zero, Intact 20-HETE 10−7 ** p < 0.05 vs. TBI 20-HETE 10−7 and Intact U46619 10−7, Intact U46619 10−6 ** p < 0.05 TBI U46619 10−6 Ʃn= 24, n = 6 in each group). Full article ">Figure 6
This figure shows the role of impaired pressure- and flow-sensitive mechanisms in the development of traumatic brain injury (TBI)-induced vasomotor dysfunction and brain edema. In normal, intact conditions, pressure- and flow-sensitive mechanisms maintain—in a wide range—a relatively constant cerebral blood flow despite of increasing perfusion pressure (autoregulation). After TBI, the impairment of these mechanisms develops, thus we propose that blood flow would increase as a function of pressure. In addition, in the lack of appropriate constrictions of larger and smaller arteries—not only CBF, intracranial volume and thus pressure increases as perfusion pressure increases—but also the distal microvessels—part of the blood brain barrier—become exposed to higher intraluminal pressure. These, together with the mediators released from the injured brain tissue, could lead to the opening of BBB, leakage of fluid, and various molecules, contributing to the development of edema and brain tissue injury. Full article ">

15 pages, 697 KiB

Open AccessReview

Improvement of Glucose Tolerance by Food Factors Having Glucagon-Like Peptide-1 Releasing Activity

by Tohru Hira, Aphichat Trakooncharoenvit, Hayate Taguchi and Hiroshi Hara

Int. J. Mol. Sci. 2021, 22(12), 6623; https://doi.org/10.3390/ijms22126623 - 21 Jun 2021

Cited by 17 | Viewed by 11208

Abstract

Glucagon-like peptide-1 (GLP-1) is a gastrointestinal hormone released from enteroendocrine L cells in response to meal ingestion. GLP-1 receptor agonists and GLP-1 enhancers have been clinically employed to treat diabetes owing to their glucose-dependent insulin-releasing activity. The release of GLP-1 is primarily stimulated [...] Read more.

Glucagon-like peptide-1 (GLP-1) is a gastrointestinal hormone released from enteroendocrine L cells in response to meal ingestion. GLP-1 receptor agonists and GLP-1 enhancers have been clinically employed to treat diabetes owing to their glucose-dependent insulin-releasing activity. The release of GLP-1 is primarily stimulated by macronutrients such as glucose and fatty acids, which are nutritionally indispensable; however, excessive intake of sugar and fat is responsible for the development of obesity and diabetes. Therefore, GLP-1 releasing food factors, such as dietary peptides and non-nutrients, are deemed desirable for improving glucose tolerance. Human and animal studies have revealed that dietary proteins/peptides have a potent effect on stimulating GLP-1 secretion. Studies in enteroendocrine cell models have shown that dietary peptides, amino acids, and phytochemicals, such as quercetin, can directly stimulate GLP-1 secretion. In our animal experiments, these food factors improved glucose metabolism and increased GLP-1 secretion. Furthermore, some dietary peptides not only stimulated GLP-1 secretion but also reduced plasma peptidase activity, which is responsible for GLP-1 inactivation. Herein, we review the relationship between GLP-1 and food factors, especially dietary peptides and flavonoids. Accordingly, utilization of food factors with GLP-1-releasing/enhancing activity is a promising strategy for preventing and treating obesity and diabetes. Full article

(This article belongs to the Special Issue The Effect of Phytochemicals and Food Bioactive Compounds on Diabetes)

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15 pages, 2309 KiB

Open AccessArticle

Telomere Length in Chromosomally Normal and Abnormal Miscarriages and Ongoing Pregnancies and Its Association with 5-hydroxymethylcytosine Patterns

by Mikhail I. Krapivin, Andrei V. Tikhonov, Olga A. Efimova, Anna A. Pendina, Anna A. Smirnova, Olga G. Chiryaeva, Olga E. Talantova, Lubov’ I. Petrova, Vera S. Dudkina and Vladislav S. Baranov

Int. J. Mol. Sci. 2021, 22(12), 6622; https://doi.org/10.3390/ijms22126622 - 21 Jun 2021

Cited by 5 | Viewed by 2397

Abstract

The present study investigates telomere length (TL) in dividing chorionic cytotrophoblast cells from karyotypically normal and abnormal first trimester miscarriages and ongoing pregnancies. Using Q-FISH, we measured relative TLs in the metaphase chromosomes of 61 chorionic villous samples. Relative TLs did not differ [...] Read more.

The present study investigates telomere length (TL) in dividing chorionic cytotrophoblast cells from karyotypically normal and abnormal first trimester miscarriages and ongoing pregnancies. Using Q-FISH, we measured relative TLs in the metaphase chromosomes of 61 chorionic villous samples. Relative TLs did not differ between karyotypically normal samples from miscarriages and those from ongoing pregnancies (p = 0.3739). However, among the karyotypically abnormal samples, relative TLs were significantly higher in ongoing pregnancies than in miscarriages (p < 0.0001). Relative TLs were also significantly higher in chorion samples from karyotypically abnormal ongoing pregnancies than in those from karyotypically normal ones (p = 0.0018) in contrast to miscarriages, where relative TL values were higher in the karyotypically normal samples (p = 0.002). In the karyotypically abnormal chorionic cytotrophoblast, the TL variance was significantly lower than in any other group (p < 0.05). Assessed by TL ratios between sister chromatids, interchromatid TL asymmetry demonstrated similar patterns across all of the chorion samples (p = 0.22) but significantly exceeded that in PHA-stimulated lymphocytes (p < 0.0001, p = 0.0003). The longer telomere was predominantly present in the hydroxymethylated sister chromatid in chromosomes featuring hemihydroxymethylation (containing 5-hydroxymethylcytosine in only one sister chromatid)—a typical sign of chorionic cytotrophoblast cells. Our results suggest that the phenomena of interchromatid TL asymmetry and its association to 5hmC patterns in chorionic cytotrophoblast, which are potentially linked to telomere lengthening through recombination, are inherent to the development programme. The TL differences in chorionic cytotrophoblast that are associated with karyotype and embryo viability seem to be determined by heredity rather than telomere elongation mechanisms. The inheritance of long telomeres by a karyotypically abnormal embryo promotes his development, whereas TL in karyotypically normal first-trimester embryos does not seem to have a considerable impact on developmental capacity. Full article

(This article belongs to the Special Issue Structural Variations of the Genome)

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Figure 1
Column bar charts of 16p subtelomeric fluorescence intensity in the metaphase chromosomes from chorionic cytotrophoblast cells in karyotypically normal and abnormal miscarriages and ongoing pregnancies. The Kruskal–Wallis test showed no significant difference among the groups (p = 0.21). Full article ">Figure 2
The correlation between the mean relative telomere length (TL) of chromosome 16 homologues and that of other chromosomes in the same metaphase assessed in 107 metaphases across 10 chorionic cytotrophoblast samples (Spearman test, ρ = 0.915; p < 0.0001). Full article ">Figure 3
Telomere detection in the metaphase chromosomes from chorionic cytotrophoblast cells in karyotypically normal (A,B) and abnormal (C,D) miscarriages (B,D) and ongoing pregnancies (A,C). Telomeres were detected through fluorescent in situ hybridisation (FISH) with telomeric DNA probes, and the chromosomes were stained with DAPI. Full article ">Figure 4
Mean relative telomere lengths (TLs) in metaphase chromosomes from chorionic cytotrophoblast in karyotypically normal and abnormal miscarriages and ongoing pregnancies. The comparisons showing significant difference (the Mann–Whitney U test) are framed. Full article ">Figure 5
Interindividual variability of mean relative telomere lengths (TLs) in metaphase chromosomes from chorionic cytotrophoblast in karyotypically normal and abnormal miscarriages and ongoing pregnancies. In karyotypically abnormal chorionic cytotrophoblast the TL variance is significantly lower than in other groups under study (p < 0.05). Full article ">Figure 6
Column bar charts of telomere length (TL) ratios between the sister chromatids of chromosomes 16 in the chorionic cytotrophoblast from miscarriages and ongoing pregnancies and in PHA-stimulated peripheral blood lymphocytes of healthy adults. TL ratios do not differ among karyotypically normal and abnormal chorionic cytotrophoblast samples from miscarriages and ongoing pregnancies (the Kruskal–Wallis test, p = 0.22). Still, they are significantly higher than those in PHA-stimulated lymphocytes (the Mann–Whitney U test, p < 0.0001, p = 0.0003). Full article ">Figure 7
The metaphase plate from a chorionic cytotrophoblast cell after immunocytochemical detection of 5-hydroxymethylcytosine (5hmC) (A) and detection of telomeric regions through fluorescent in situ hybridisation (FISH) with telomeric DNA probes (B). The chromosomes were stained with DAPI. The arrows show chromosomes represented on karyogram (C): those demonstrating the asymmetrical pattern of hydroxymethylation with 5hmC in only one sister chromatid—hemihydroxymethylation. Full article ">

18 pages, 5975 KiB

Open AccessArticle

Electrophysiology of hiPSC-Cardiomyocytes Co-Cultured with HEK Cells Expressing the Inward Rectifier Channel

by Ana Da Silva Costa, Peter Mortensen, Maria P. Hortigon-Vinagre, Marcel A. G. van der Heyden, Francis L. Burton, Hao Gao, Radostin D. Simitev and Godfrey L. Smith

Int. J. Mol. Sci. 2021, 22(12), 6621; https://doi.org/10.3390/ijms22126621 - 21 Jun 2021

Cited by 4 | Viewed by 3589

Abstract

The immature electrophysiology of human-induced pluripotent stem cell-derived cardiomyocytes (hiCMs) complicates their use for therapeutic and pharmacological purposes. An insufficient inward rectifying current (I_K1) and the presence of a funny current (if) cause spontaneous electrical activity. This study tests the hypothesis [...] Read more.

The immature electrophysiology of human-induced pluripotent stem cell-derived cardiomyocytes (hiCMs) complicates their use for therapeutic and pharmacological purposes. An insufficient inward rectifying current (I_K1) and the presence of a funny current (if) cause spontaneous electrical activity. This study tests the hypothesis that the co-culturing of hiCMs with a human embryonic kidney (HEK) cell-line expressing the Kir2.1 channel (HEK-I_K1) can generate an electrical syncytium with an adult-like cardiac electrophysiology. The mechanical activity of co-cultures using different HEK-I_K1:hiCM ratios was compared with co-cultures using wildtype (HEK–WT:hiCM) or hiCM alone on days 3–8 after plating. Only ratios of 1:3 and 1:1 showed a significant reduction in spontaneous rate at days 4 and 6, suggesting that I_K1 was influencing the electrophysiology. Detailed analysis at day 4 revealed an increased incidence of quiescent wells or sub-areas. Electrical activity showed a decreased action potential duration (APD) at 20% and 50%, but not at 90%, alongside a reduced amplitude of the aggregate AP signal. A computational model of the 1:1 co-culture replicates the electrophysiological effects of HEK–WT. The addition of the I_K1 conductance reduced the spontaneous rate and APD20, 50 and 90, and minor variation in the intercellular conductance caused quiescence. In conclusion, a 1:1 co-culture HEK-I_K1:hiCM caused changes in electrophysiology and spontaneous activity consistent with the integration of I_K1 into the electrical syncytium. However, the additional electrical effects of the HEK cell at 1:1 increased the possibility of electrical quiescence before sufficient I_K1 was integrated into the syncytium. Full article

(This article belongs to the Special Issue hiPSC-Derived Cells as Models for Drug Discovery 2.0)

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Figure 1
The effects of co-cultures of hiCMs with increasing densities of HEK, for both HEK-IK1:hiCM and HEK–WT:hiCM. (A) Example traces of the effects of 1:30 and 1:1 at days 4 and 8. (Bi) Frequency of spontaneous contraction at days 4 to 8 with the ratio 1:30; (Bii) frequency at the 1:10 ratio; (Biii) frequency at the 1:3 ratio; (Biv) frequency at the 1:1 ratio; (C) frequency as a percentage from baseline (standard hiCM culture) for the range of ratios. (Ci) Day 4; (Cii) day 6; (Ciii) day 8. (D) Contraction duration (CD50) on days 4, 6 and 8 comparing hiCM culture, HEK–WT:hiCM and HEK-IK1:hiCM. One-way ANOVA with Bartlett’s test, * p < 0.05, n = 51 wells. Full article ">Figure 2
Cell movement effects of the 1:1 co-culture on day 4 in vitro in serum-free conditions, showing observations from individual experiments. Each plating is shown in a different color, and data are presented as mean+/−SD. (A) Frequency of spontaneous contraction. (B) Amplitude of the spontaneous contraction. (C) Time to contract at (Ci) spontaneous, (Cii) 1 Hz, and (Ciii) 2 Hz conditions. (D) Time to relax at (Di) spontaneous, (Dii) 1 Hz, and (Diii) 2 Hz. (E) This shows 50% of the contraction duration at (Ei) spontaneous, (Eii) 1 Hz, and (Eiii) 2 Hz. The comparison of each culture (hiCM, HEK–WT:hiCM and HEK-IK1:hiCM) within each experiment is shown as # in the respective experimental, and 2-way ANOVA was used for statistical analysis. The mean of all experiments was then compared using a paired t-test and this is shown as * (p < 0.05). Full article ">Figure 3
Spatial analysis of 1:1 HEK:CM on day 4 in culture in serum-free medium. (A) Example images obtained using spatial analysis of contractile motion. A heat map showing amplitudes recorded in a 200 × 200 µm area using a 10 × 10 grid were derived from the brightfield image (left). The colors represent the amplitude of the contraction in each square. Contraction signals from all sites and the average contraction are also shown. (B) Percentage of active sites representing contractile cells in a 200 × 200 µm area. (C) The amplitude of the contraction determined by pixel displacement. (D) Mean of range of amplitudes across a 10 × 10 grid. Unpaired t-test: HEK-IK1 vs. HEK–WT (black) and hiCM vs. HEK–WT (blue) or HEK-IK1 (red). *** p < 0.001, ** p < 0.01, * p < 0.05, n > 28 cells, 5 platings. Full article ">Figure 4
Electrophysiological effects of 1:1 co-culture on day 4 in vitro in serum-free conditions, showing the observations from individual experiments. Each plating is shown in a different color, and data are presented as mean+/−SD. (A) Frequency of spontaneous beating. (B) Amplitude of the AP. (C) APD20 at (Ci) spontaneous, (Cii) 1Hz, and (Ciii) 2Hz. (D) APD50 at (Di) spontaneous, (Dii) 1 Hz, and (Diii) 2 Hz. (E) APD90 at (Ei) spontaneous, (Eii) 1 Hz, and (Eiii) 2 Hz. Due to the small AP amplitude and low signal-to-noise ratio (SNR) (<a href="#app1-ijms-22-06621" class="html-app">Supplementary Figure S3</a>) in HEK-IK1:hiCM, fewer data are available for APD90 at spontaneous rates. Comparison of each culture (hiCM, HEK–WT:hiCM and HEK-IK1:hiCM) within each experiment is shown as # in the respective experimental color, and 2-way ANOVA was used for statistical analysis. The mean of all experiments was then compared using a paired t-test and this is shown with * (p < 0.05). Full article ">Figure 5
Computational modeling shows the effects of varying gap junction conductance (Ggap) in a co-culture of hiCM with HEK–WT, and different Na+ channel expression. (A) Diagram of HEK:hiCM interaction used for computational model. (B) Example trace showing hiCM potential, HEK potential, and the average of the two. (C) Varying Ggap effects on frequency of spontaneous beating, hiCM’s Vmin, amplitude and APD. Simulations were done in regular INa (1 × INa) and when only half (0.5 × INa) was present. Full article ">Figure 6
Computational modeling shows the effects of varying gap junction conductance (Ggap) and IK1 conductance (GIK1) in co-cultures of hiCM with HEK-IK1 and different Na+ channel expressions. (A) Diagram of HEK:hiCM interaction used for computational model. (B) Example trace showing hiCM potential, HEK potential, and the average of the two. (C) Different parameters are affected by varying IK1 conductance in a full INa model, and a half INa. (D) Electrophysiology is affected by increasing gap junction conductance in a co-culture of hiCM with HEK-IK1. Full article ">

4 pages, 184 KiB

Open AccessEditorial

Understanding Amyloid Structures and Disease: A Continuing Challenge in Health Research

by Grazia Chiellini

Int. J. Mol. Sci. 2021, 22(12), 6620; https://doi.org/10.3390/ijms22126620 - 21 Jun 2021

Cited by 3 | Viewed by 1926

Abstract

Neurodegenerative disorders (NDDs), including Alzheimer’s, Parkinson’s, and Huntington’s diseases, are a highly prevalent class of disorders that share the presence of aberrant aggregates called amyloids in the nervous system [...] Full article

(This article belongs to the Special Issue Understanding Amyloid Structures and Disease: A Continuing Challenge in Health Research)

30 pages, 1194 KiB

Open AccessReview

Objective and Measurable Biomarkers in Chronic Subjective Tinnitus

by Dae-Woong Kang, Sung-Soo Kim, Dong-Choon Park, Sang-Hoon Kim and Seung-Geun Yeo

Int. J. Mol. Sci. 2021, 22(12), 6619; https://doi.org/10.3390/ijms22126619 - 21 Jun 2021

Cited by 19 | Viewed by 5672

Abstract

Tinnitus is associated with increased social costs and reduced quality of life through sleep disorders or psychological distress. The pathophysiology of chronic subjective tinnitus, which accounts for most tinnitus, has not been clearly elucidated. This is because chronic subjective tinnitus is difficult to [...] Read more.

Tinnitus is associated with increased social costs and reduced quality of life through sleep disorders or psychological distress. The pathophysiology of chronic subjective tinnitus, which accounts for most tinnitus, has not been clearly elucidated. This is because chronic subjective tinnitus is difficult to evaluate objectively, and there are no objective markers that represent the diagnosis or therapeutic effect of tinnitus. Based on the results of studies on patients with chronic subjective tinnitus, objective and measurable biomarkers that help to identify the pathophysiology of tinnitus have been summarized. A total of 271 studies in PubMed, 303 in EMBASE, and 45 in Cochrane Library were found on biomarkers related to chronic subjective tinnitus published until April 2021. Duplicate articles, articles not written in English, review articles, case reports, and articles that did not match our topic were excluded. A total of 49 studies were included. Three specimens, including blood, saliva, and urine, and a total of 58 biomarkers were used as indicators for diagnosis, evaluation, prognosis, and therapeutic effectiveness of tinnitus. Biomarkers were classified into eight categories comprising metabolic, hemostatic, inflammatory, endocrine, immunological, neurologic, and oxidative parameters. Biomarkers can help in the diagnosis, measure the severity, predict prognosis, and treatment outcome of tinnitus. Full article

(This article belongs to the Special Issue Biomarkers in Rare Diseases 2.0)

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23 pages, 3081 KiB

Open AccessArticle

Functionalization of Photosensitized Silica Nanoparticles for Advanced Photodynamic Therapy of Cancer

by Ruth Prieto-Montero, Alejandro Prieto-Castañeda, Alberto Katsumiti, Miren P. Cajaraville, Antonia R. Agarrabeitia, María J. Ortiz and Virginia Martínez-Martínez

Int. J. Mol. Sci. 2021, 22(12), 6618; https://doi.org/10.3390/ijms22126618 - 21 Jun 2021

Cited by 14 | Viewed by 4919

Abstract

BODIPY dyes have recently attracted attention as potential photosensitizers. In this work, commercial and novel photosensitizers (PSs) based on BODIPY chromophores (haloBODIPYs and orthogonal dimers strategically designed with intense bands in the blue, green or red region of the visible spectra and high [...] Read more.

BODIPY dyes have recently attracted attention as potential photosensitizers. In this work, commercial and novel photosensitizers (PSs) based on BODIPY chromophores (haloBODIPYs and orthogonal dimers strategically designed with intense bands in the blue, green or red region of the visible spectra and high singlet oxygen production) were covalently linked to mesoporous silica nanoparticles (MSNs) further functionalized with PEG and folic acid (FA). MSNs approximately 50 nm in size with different functional groups were synthesized to allow multiple alternatives of PS-PEG-FA decoration of their external surface. Different combinations varying the type of PS (commercial Rose Bengal, Thionine and Chlorine e6 or custom-made BODIPY-based), the linkage design, and the length of PEG are detailed. All the nanosystems were physicochemically characterized (morphology, diameter, size distribution and PS loaded amount) and photophysically studied (absorption capacity, fluorescence efficiency, and singlet oxygen production) in suspension. For the most promising PS-PEG-FA silica nanoplatforms, the biocompatibility in dark conditions and the phototoxicity under suitable irradiation wavelengths (blue, green, or red) at regulated light doses (10–15 J/cm²) were compared with PSs free in solution in HeLa cells in vitro. Full article

(This article belongs to the Special Issue Nanomaterials in Cancer Diagnosis and Therapy)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
Molecular structure of the different compounds anchored to MSN: commercial (RB, Th, C6) and custom-made BODIPY photosensitizers (BDP1-BDP7), PEG derivatives with different functional groups (Si-PEG and NHS-PEG) and molecular weight (750 Da, 2000 Da and 5000 Da), and FA. Full article ">Figure 2
TEM images of MSNs. There are no noticeable differences between any of the synthesized MSNs (NH-MSN, CN-MSN and COOH-MSN). Full article ">Figure 3
Normalized absorption spectra of RB-PEG2000-NP-a (red), RB-PEG5000-NP-a (brown), RB-PEG-NP-b (blue), RB-PEG-NP-c (black), RB-PEG-NP-d (purple) in water suspension (0.5 mg/mL) and RB in diluted aqueous solution (green). The absorption spectra were recorded after stirring the nanosystems for at least 24 h. Full article ">Figure 4
Cell viability (MTT assay) of HeLa cells exposed to different RB concentrations, (A) in solution, and (B) tethered at MNS (sample RB-PEG-NP-d) under dark conditions (blue bars) and green irradiation at 518 nm and 10 J/cm2 (orange bars). Stars indicate significant differences with respect to controls. Asterisks indicate significant differences between dark and light conditions at the same concentrations tested. Full article ">Figure 5
Confocal fluorescence microscopy images (λex = 561 nm and λem = 565–615 nm) of HeLa cells exposed to RB free in solution (A–C) and cells exposed to RB-PEG-NP-d (D–I) at the same RB concentration (1 μM). Scale bars = 100 μm. Full article ">Figure 6
Normalized absorption spectra of PS in CHCl3 solution (brown) and the PS tethered at the external surface of MSN together with PEG and FA (black) in CH3OH at 0.5 mg/mL. The absorption spectra for all the PS-MSN samples were recorded after stirring the nanosystems for at least 24 h. Full article ">Figure 7
Cell viability (MTT assay) of HeLa cells exposed to the PSs in solution BDP2 (A) and BDP4 (C) and to their corresponding nanosystems BDP3-NP (B) and BDP5-NP (D) under dark conditions (blue bars) and after green irradiation at 10 J/cm2 (orange bars). Stars indicate significant differences with respect to controls. Asterisks indicate significant differences between dark and light conditions at the same concentrations tested. Full article ">Figure 8
Cell viability (MTT assay) of HeLa cells exposed to PSs in solution C6 (A) and BDP6 (C) and to their respective the nanosystems C6-NP (B), and BDP6-NP (D) under dark conditions (blue bars) and after red irradiation at 15 J/cm2 (orange bars). Stars indicate significant differences with respect to controls. Asterisks indicate significant differences between dark and light conditions at the same concentrations tested. Full article ">

14 pages, 1739 KiB

Open AccessReview

From Genetic Mutations to Molecular Basis of Heart Failure Treatment: An Overview of the Mechanism and Implication of the Novel Modulators for Cardiac Myosin

by Yu-Jen Chen, Chian-Shiu Chien, Chern-En Chiang, Chen-Huan Chen and Hao-Min Cheng

Int. J. Mol. Sci. 2021, 22(12), 6617; https://doi.org/10.3390/ijms22126617 - 21 Jun 2021

Cited by 11 | Viewed by 6768

Abstract

Heart failure (HF) is a syndrome encompassing several important etiologies that lead to the imbalance between oxygen demand and supply. Despite the usage of guideline-directed medical therapy for HF has shown better outcomes, novel therapeutic strategies are desirable, especially for patients with preserved [...] Read more.

Heart failure (HF) is a syndrome encompassing several important etiologies that lead to the imbalance between oxygen demand and supply. Despite the usage of guideline-directed medical therapy for HF has shown better outcomes, novel therapeutic strategies are desirable, especially for patients with preserved or mildly reduced left ventricular ejection fraction. In this regard, understanding the molecular basis for cardiomyopathies is expected to fill in the knowledge gap and generate new therapies to improve prognosis for HF. This review discusses an evolutionary mechanism designed to regulate cardiac contraction and relaxation through the most often genetically determined cardiomyopathies associated with HF. In addition, both the myosin inhibitor and myosin activator are promising new treatments for cardiomyopathies. A comprehensive review from genetic mutations to the molecular basis of direct sarcomere modulators will help shed light on future studies for a better characterization of HF etiologies and potential therapeutic targets. Full article

(This article belongs to the Special Issue Heart Failure: From Molecular Basis to Therapy 2.0)

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Figure 1
Pharmacological and interventional treatment for heart failure with reduced ejection fraction: The red arrows indicate a combination of the four drugs that should be initiated early in HFrEF patients. The dotted arrows indicate the additional drugs and interventional therapies for individualized treatment for specific populations. Full article ">Figure 2
Cardiac excitation-contraction coupling: Action potential transmits directly from adjacent cells (step 1). Calcium enters cardiomyocyte through voltage-gated L-type Ca2+ channels (step 2). The initial influx of Ca2+ stimulates efflux of Ca2+ from ryanodine receptor type-2 channels on the sarcoplasmic reticulum (step 3) resulting in contraction of the heart (step 4). As the contraction ends (step 5), the Ca2+ reuptake is completed by sarcoplasmic/endoplasmic reticulum Ca2+-ATPase 2a (SERCA2a) (step 6). The sodium-calcium exchanger removes Ca2+ from cells (step 7). Full article ">Figure 3
(Panel A): A schematic of two myosin conformations and associated energy consumption throughout the cardiac cycle: A pair of myosin molecules is depicted, with each head denoted as blocked (BH) or free (FH). The disordered relaxed state (DRX) insulates the BH, resulting in inhibition of ATPase (denoted by a blue dot), while FH retains adenosine triphosphate (ATP) hydrolysis activity and triggers actomyosin function modulating by myosin binding protein C (MyBPC). The super-relaxed state (SRX) insulates both BH and FH, and energy conservation is maximized because both myosin ATPase domains are inhibited. Hypertrophic cardiomyopathy variants preferentially shift conformation toward the DRX, resulting in hypercontractility, impaired relaxation, and excessive energy consumption. Mavacamten can stabilize the SRX state, attenuate hypercontractility, and improve compliance in cardiomyocytes. (Panel B): Biochemical cycle of cardiac myosin. During diastole, one head of myosin hydrolyzes ATP to adenosine diphosphate (ADP) and inorganic phosphate (Pi) (Step 1). Actin becomes accessible, and the head of myosin binds to it and forms the “pre-powerstroke” state. During systole, a subset of myosin heads in the pre-powerstroke promotes the release of Pi (Step 2), which initiates the “powerstroke” to generate force, shortening the sarcomere. (Step 3). The loss of ADP and another binding of ATP (Step 4) releases the myosin from the actin filament because myosin-ATP has a low affinity for actin (Step 5). Omecamtiv mecarbil increases the rate of Pi release (Step 2) and bias the ATP hydrolysis step (Step 1) toward pre-powerstroke state, enabling more myosin heads to undergo a powerstroke during systole. Full article ">Figure 3 Cont.
(Panel A): A schematic of two myosin conformations and associated energy consumption throughout the cardiac cycle: A pair of myosin molecules is depicted, with each head denoted as blocked (BH) or free (FH). The disordered relaxed state (DRX) insulates the BH, resulting in inhibition of ATPase (denoted by a blue dot), while FH retains adenosine triphosphate (ATP) hydrolysis activity and triggers actomyosin function modulating by myosin binding protein C (MyBPC). The super-relaxed state (SRX) insulates both BH and FH, and energy conservation is maximized because both myosin ATPase domains are inhibited. Hypertrophic cardiomyopathy variants preferentially shift conformation toward the DRX, resulting in hypercontractility, impaired relaxation, and excessive energy consumption. Mavacamten can stabilize the SRX state, attenuate hypercontractility, and improve compliance in cardiomyocytes. (Panel B): Biochemical cycle of cardiac myosin. During diastole, one head of myosin hydrolyzes ATP to adenosine diphosphate (ADP) and inorganic phosphate (Pi) (Step 1). Actin becomes accessible, and the head of myosin binds to it and forms the “pre-powerstroke” state. During systole, a subset of myosin heads in the pre-powerstroke promotes the release of Pi (Step 2), which initiates the “powerstroke” to generate force, shortening the sarcomere. (Step 3). The loss of ADP and another binding of ATP (Step 4) releases the myosin from the actin filament because myosin-ATP has a low affinity for actin (Step 5). Omecamtiv mecarbil increases the rate of Pi release (Step 2) and bias the ATP hydrolysis step (Step 1) toward pre-powerstroke state, enabling more myosin heads to undergo a powerstroke during systole. Full article ">

27 pages, 2905 KiB

Open AccessReview

On the Use of Surface Plasmon Resonance Biosensing to Understand IgG-FcγR Interactions

by Catherine Forest-Nault, Jimmy Gaudreault, Olivier Henry, Yves Durocher and Gregory De Crescenzo

Int. J. Mol. Sci. 2021, 22(12), 6616; https://doi.org/10.3390/ijms22126616 - 21 Jun 2021

Cited by 25 | Viewed by 4788

Abstract

Surface plasmon resonance (SPR)-based optical biosensors offer real-time and label-free analysis of protein interactions, which has extensively contributed to the discovery and development of therapeutic monoclonal antibodies (mAbs). As the biopharmaceutical market for these biologics and their biosimilars is rapidly growing, the role [...] Read more.

Surface plasmon resonance (SPR)-based optical biosensors offer real-time and label-free analysis of protein interactions, which has extensively contributed to the discovery and development of therapeutic monoclonal antibodies (mAbs). As the biopharmaceutical market for these biologics and their biosimilars is rapidly growing, the role of SPR biosensors in drug discovery and quality assessment is becoming increasingly prominent. One of the critical quality attributes of mAbs is the N-glycosylation of their Fc region. Other than providing stability to the antibody, the Fc N-glycosylation influences immunoglobulin G (IgG) interactions with the Fcγ receptors (FcγRs), modulating the immune response. Over the past two decades, several studies have relied on SPR-based assays to characterize the influence of N-glycosylation upon the IgG-FcγR interactions. While these studies have unveiled key information, many conclusions are still debated in the literature. These discrepancies can be, in part, attributed to the design of the reported SPR-based assays as well as the methodology applied to SPR data analysis. In fact, the SPR biosensor best practices have evolved over the years, and several biases have been pointed out in the development of experimental SPR protocols. In parallel, newly developed algorithms and data analysis methods now allow taking into consideration complex biomolecular kinetics. In this review, we detail the use of different SPR biosensing approaches for characterizing the IgG-FcγR interactions, highlighting their merit and inherent experimental complexity. Furthermore, we review the latest SPR-derived conclusions on the influence of the N-glycosylation upon the IgG-FcγR interactions and underline the differences and similarities across the literature. Finally, we explore new avenues taking advantage of novel computational analysis of SPR results as well as the latest strategies to control the glycoprofile of mAbs during production, which could lead to a better understanding and modelling of the IgG-FcγRs interactions. Full article

(This article belongs to the Special Issue Fc Receptors)

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Figure 1
Trastuzumab (analyte) binding to FcγRIIIaV158 (ligand) recorded with a Biacore T100 instrument. Triplicate injections of six concentrations of Trastuzumab (20, 100, 250, 500, 1000, and 2000 nM) and buffer injection as blank were performed for 300 s, followed by 480 s of running buffer injection. The experiment is run over two surfaces: (A) an experimental surface presenting 20 RU of FcγRIIIaV158 immobilized and (B) a mock surface. (C) Control-corrected sensorgram resulting from the subtraction of data measured on the mock surface from the experimental surface data. The control-corrected data of the blank (D) is then subtracted from the experimental control-corrected data resulting in a double-referenced sensorgram (E). Full article ">Figure 2
Affinities reported in the literature between FcγRs and IgGs (35 studies). The red line crosses the median point values specific to each receptor. Full article ">Figure 3
Affinities reported in the literature between IgG and (A) FcgRI, (B) FcgRIIa, (C) FcgRIIb, (D) FcgRIIIaF158, and (E) FcgRIIIaV158 depending on the analysis model (steady-state or 1:1 Langmuir kinetic model). The blue line represents the median of all values combined, while the red line crosses the median point values specific to each analysis model. Full article ">Figure 4
Affinities reported in the literature between IgG and (A) FcγRI, (B) FcγRIIa, (C) FcγRIIb, (D) FcγRIIIaF158 and (E) FcγRIIIaV158 depending on the immobilization strategy. GFAHK stands for Goat F(ab′)2 anti-human kappa antibody. The blue line represents the median of all values combined, while the red line crosses the median point values specific to each immobilization strategy. Full article ">

22 pages, 4803 KiB

Open AccessArticle

Recent Developments on gMicroMC: Transport Simulations of Proton and Heavy Ions and Concurrent Transport of Radicals and DNA

by Youfang Lai, Xun Jia and Yujie Chi

Int. J. Mol. Sci. 2021, 22(12), 6615; https://doi.org/10.3390/ijms22126615 - 21 Jun 2021

Cited by 6 | Viewed by 2913

Abstract

Mechanistic Monte Carlo (MC) simulation of radiation interaction with water and DNA is important for the understanding of biological responses induced by ionizing radiation. In our previous work, we employed the Graphical Processing Unit (GPU)-based parallel computing technique to develop a novel, highly [...] Read more.

Mechanistic Monte Carlo (MC) simulation of radiation interaction with water and DNA is important for the understanding of biological responses induced by ionizing radiation. In our previous work, we employed the Graphical Processing Unit (GPU)-based parallel computing technique to develop a novel, highly efficient, and open-source MC simulation tool, gMicroMC, for simulating electron-induced DNA damages. In this work, we reported two new developments in gMicroMC: the transport simulation of protons and heavy ions and the concurrent transport of radicals in the presence of DNA. We modeled these transports based on electromagnetic interactions between charged particles and water molecules and the chemical reactions between radicals and DNA molecules. Various physical properties, such as Linear Energy Transfer (LET) and particle range, from our simulation agreed with data published by NIST or simulation results from other CPU-based MC packages. The simulation results of DNA damage under the concurrent transport of radicals and DNA agreed with those from nBio-Topas simulation in a comprehensive testing case. GPU parallel computing enabled high computational efficiency. It took 41 s to simultaneously transport 100 protons with an initial kinetic energy of 10 MeV in water and 470 s to transport 10

^{5}

radicals up to 1 µs in the presence of DNA. Full article

(This article belongs to the Special Issue Advances in Molecular Simulation)

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18 pages, 1004 KiB

Open AccessReview

THE MAIN CYTOTOXIC EFFECTS OF METHYLSELENINIC ACID ON VARIOUS CANCER CELLS

by Elena G. Varlamova and Egor A. Turovsky

Int. J. Mol. Sci. 2021, 22(12), 6614; https://doi.org/10.3390/ijms22126614 - 21 Jun 2021

Cited by 37 | Viewed by 3353

Abstract

Studies of recent decades have repeatedly demonstrated the cytotoxic effect of selenium-containing compounds on cancer cells of various origins. Particular attention in these studies is paid to methylseleninic acid, a widespread selenium-containing compound of organic nature, for several reasons: it has a selective [...] Read more.

Studies of recent decades have repeatedly demonstrated the cytotoxic effect of selenium-containing compounds on cancer cells of various origins. Particular attention in these studies is paid to methylseleninic acid, a widespread selenium-containing compound of organic nature, for several reasons: it has a selective cytotoxic effect on cancer cells, it is cytotoxic in small doses, it is able to generate methylselenol, excluding the action of the enzyme β-lyase. All these qualities make methylseleninic acid an attractive substrate for the production of anticancer drugs on its basis with a well-pronounced selective effect. However, the studies available to date indicate that there is no strictly specific molecular mechanism of its cytotoxic effect in relation to different cancer cell lines and cancer models. This review contains generalized information on the dose- and time-dependent regulation of the toxic effect of methylseleninic acid on the proliferative properties of a number of cancer cell lines. In addition, special attention in this review is paid to the influence of this selenium-containing compound on the regulation of endoplasmic reticulum stress and on the expression of seven selenoproteins, which are localized in the endoplasmic reticulum. Full article

(This article belongs to the Special Issue Epigenetics in Molecular Toxicology)

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Int. J. Mol. Sci., Volume 22, Issue 12 (June-2 2021) – 476 articles

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