Biomolecules

19 pages, 2962 KiB

Open AccessArticle

Comparative Study of Transcriptome in the Hearts Isolated from Mice, Rats, and Humans

by Daigo Okada, Yosuke Okamoto, Toshiro Io, Miho Oka, Daiki Kobayashi, Suzuka Ito, Ryo Yamada, Kuniaki Ishii and Kyoichi Ono

Biomolecules 2022, 12(6), 859; https://doi.org/10.3390/biom12060859 - 20 Jun 2022

Cited by 4 | Viewed by 2981

Abstract

The heart is a significant organ in mammalian life, and the heartbeat mechanism has been an essential focus of science. However, few studies have focused on species differences. Accordingly, challenges remain in studying genes that have universal functions across species and genes that [...] Read more.

The heart is a significant organ in mammalian life, and the heartbeat mechanism has been an essential focus of science. However, few studies have focused on species differences. Accordingly, challenges remain in studying genes that have universal functions across species and genes that determine species differences. Here, we analyzed transcriptome data in mouse, rat, and human atria, ventricles, and sinoatrial nodes (SA) obtained from different platforms and compared them by calculating specificity measure (SPM) values in consideration of species differences. Among the three heart regions, the species differences in SA were the greatest, and we searched for genes that determined the essential characteristics of SA, which was SHOX2 in our criteria. The SPM value of SHOX2 was prominently high across species. Similarly, by calculating SPM values, we identified 3 atrial-specific, 11 ventricular-specific, and 17 SA-specific markers. Ontology analysis identified 70 cardiac region- and species-specific ontologies. These results suggest that reanalyzing existing data by calculating SPM values may identify novel tissue-specific genes and species-dependent gene expression. This study identified the importance of SHOX2 as an SA-specific transcription factor, a novel cardiac regional marker, and species-dependent ontologies. Full article

(This article belongs to the Special Issue Molecular Pathogenesis of Cardiac Arrhythmia)

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12 pages, 10063 KiB

Open AccessReview

Biochemical Properties and Physiological Functions of pLG72: Twenty Years of Investigations

by Giulia Murtas, Loredano Pollegioni, Gianluca Molla and Silvia Sacchi

Biomolecules 2022, 12(6), 858; https://doi.org/10.3390/biom12060858 - 20 Jun 2022

Cited by 4 | Viewed by 2509

Abstract

In 2002, the novel human gene G72 was associated with schizophrenia susceptibility. This gene encodes a small protein of 153 amino acids, named pLG72, which represents a rare case of primate-specific protein. In particular, the rs2391191 single nucleotide polymorphism (resulting in in the [...] Read more.

In 2002, the novel human gene G72 was associated with schizophrenia susceptibility. This gene encodes a small protein of 153 amino acids, named pLG72, which represents a rare case of primate-specific protein. In particular, the rs2391191 single nucleotide polymorphism (resulting in in the R30K substitution) was robustly associated to schizophrenia and bipolar disorder. In this review, we aim to summarize the results of 20 years of biochemical investigations on pLG72. The main known role of pLG72 is related to its ability to bind and inactivate the flavoenzyme d-amino acid oxidase, i.e., the enzyme that controls the catabolism of d-serine, the main NMDA receptor coagonist in the brain. pLG72 was proposed to target the cytosolic form of d-amino acid oxidase for degradation, preserving d-serine and protecting the cell from oxidative stress generated by hydrogen peroxide produced by the flavoenzyme reaction. Anyway, pLG72 seems to play additional roles, such as affecting mitochondrial functions. The level of pLG72 in the human body is still a controversial issue because of its low expression and challenging detection. Anyway, the intriguing hypothesis that pLG72 level in blood could represent a suitable marker of Alzheimer’s disease progression (a suggestion not sufficiently established yet) merits further investigations. Full article

(This article belongs to the Special Issue Alterations in D-amino Acid Metabolism in Psychiatric and Neurological Disorders)

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13 pages, 2775 KiB

Open AccessArticle

Investigating the Effects of Dehydrated Human Amnion-Chorion Membrane on Periodontal Healing

by Kentaro Imamura, Yusuke Hamada, Wataru Yoshida, Tasuku Murakami, Saki Nakane-Koyachi, Kouki Yoshikawa and Atsushi Saito

Biomolecules 2022, 12(6), 857; https://doi.org/10.3390/biom12060857 - 20 Jun 2022

Cited by 5 | Viewed by 2459

Abstract

Each growth factor (GF) has different effects and targets, and plays a critical role in periodontal healing. Dehydrated human amnion-chorion membrane (dHACM) contains various GFs and has been used to enhance wound healing. The purpose of this study was to evaluate the effects [...] Read more.

Each growth factor (GF) has different effects and targets, and plays a critical role in periodontal healing. Dehydrated human amnion-chorion membrane (dHACM) contains various GFs and has been used to enhance wound healing. The purpose of this study was to evaluate the effects of dHACM on periodontal healing, using in vitro and in vivo experimental approaches. Standardized periodontal defects were created in rats. The defects were randomly divided into three groups: Unfilled, filled with hydroxypropyl cellulose (HPC), and dHACM+HPC. At 2 and 4 weeks postoperatively, periodontal healing was analyzed by microcomputed tomography (micro-CT), and histological and immunohistochemical analyses. In vitro, periodontal ligament-derived cells (PDLCs) isolated from rat incisors were incubated with dHACM extract. Cell proliferation and migration were evaluated by WST-1 and wound healing assay. In vivo, micro-CT examination at 2 weeks revealed enhanced formation of new bone in the dHACM+HPC group. At 4 weeks, the proportions of vascular endothelial growth factor (VEGF)-positive cells and α-smooth muscle actin (α-SMA)-positive blood vessels in the dHACM+HPC group were significantly greater than those in the Unfilled group. In vitro, dHACM extracts at 100 µg/mL significantly increased cell proliferation and migration compared with control. These findings suggest that GFs contained in dHACM promote proliferation and migration of PDLCs and angiogenesis, which lead to enhanced periodontal healing. Full article

(This article belongs to the Special Issue Advances in Basic and Clinical Periodontal Research)

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19 pages, 5390 KiB

Open AccessArticle

Phosphatidylinositol Monophosphates Regulate the Membrane Localization of HSPA1A, a Stress-Inducible 70-kDa Heat Shock Protein

by Larissa Smulders, Rachel Altman, Carolina Briseno, Alireza Saatchi, Leslie Wallace, Maha AlSebaye, Robert V. Stahelin and Nikolas Nikolaidis

Biomolecules 2022, 12(6), 856; https://doi.org/10.3390/biom12060856 - 20 Jun 2022

Cited by 5 | Viewed by 3253

Abstract

HSPA1A is a molecular chaperone that regulates the survival of stressed and cancer cells. In addition to its cytosolic pro-survival functions, HSPA1A also localizes and embeds in the plasma membrane (PM) of stressed and tumor cells. Membrane-associated HSPA1A exerts immunomodulatory functions and renders [...] Read more.

HSPA1A is a molecular chaperone that regulates the survival of stressed and cancer cells. In addition to its cytosolic pro-survival functions, HSPA1A also localizes and embeds in the plasma membrane (PM) of stressed and tumor cells. Membrane-associated HSPA1A exerts immunomodulatory functions and renders tumors resistant to standard therapies. Therefore, understanding and manipulating HSPA1A’s surface presentation is a promising therapeutic. However, HSPA1A’s pathway to the cell surface remains enigmatic because this protein lacks known membrane localization signals. Considering that HSPA1A binds to lipids, like phosphatidylserine (PS) and monophosphorylated phosphoinositides (PIPs), we hypothesized that this interaction regulates HSPA1A’s PM localization and anchorage. To test this hypothesis, we subjected human cell lines to heat shock, depleted specific lipid targets, and quantified HSPA1A’s PM localization using confocal microscopy and cell surface biotinylation. These experiments revealed that co-transfection of HSPA1A with lipid-biosensors masking PI(4)P and PI(3)P significantly reduced HSPA1A’s heat-induced surface presentation. Next, we manipulated the cellular lipid content using ionomycin, phenyl arsine oxide (PAO), GSK-A1, and wortmannin. These experiments revealed that HSPA1A’s PM localization was unaffected by ionomycin but was significantly reduced by PAO, GSK-A1, and wortmannin, corroborating the findings obtained by the co-transfection experiments. We verified these results by selectively depleting PI(4)P and PI(4,5)P₂ using a rapamycin-induced phosphatase system. Our findings strongly support the notion that HSPA1A’s surface presentation is a multifaceted lipid-driven phenomenon controlled by the binding of the chaperone to specific endosomal and PM lipids. Full article

(This article belongs to the Collection Feature Papers in Biomacromolecules: Lipids)

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23 pages, 3663 KiB

Open AccessFeature PaperArticle

Bio-Assisted Synthesis and Characterization of Zinc Oxide Nanoparticles from Lepidium sativum and Their Potent Antioxidant, Antibacterial and Anticancer Activities

by Bisma Meer, Anisa Andleeb, Junaid Iqbal, Hajra Ashraf, Kushif Meer, Joham Sarfraz Ali, Samantha Drouet, Sumaira Anjum, Azra Mehmood, Taimoor Khan, Mohammad Ali, Christophe Hano and Bilal Haider Abbasi

Biomolecules 2022, 12(6), 855; https://doi.org/10.3390/biom12060855 - 20 Jun 2022

Cited by 24 | Viewed by 3707

Abstract

Nanotechnology is an emerging area of research that deals with the production, manipulation, and application of nanoscale materials. Bio-assisted synthesis is of particular interest nowadays, to overcome the limitations associated with the physical and chemical means. The aim of this study was to [...] Read more.

Nanotechnology is an emerging area of research that deals with the production, manipulation, and application of nanoscale materials. Bio-assisted synthesis is of particular interest nowadays, to overcome the limitations associated with the physical and chemical means. The aim of this study was to synthesize ZnO nanoparticles (NPs) for the first time, utilizing the seed extract of Lepidium sativum. The synthesized NPs were confirmed through various spectroscopy and imagining techniques, such as XRD, FTIR, HPLC, and SEM. The characterized NPs were then examined for various in vitro biological assays. Crystalline, hexagonal-structured NPs with an average particle size of 25.6 nm were obtained. Biosynthesized ZnO NPs exhibited potent antioxidant activities, effective α-amylase inhibition, moderate urease inhibition (56%), high lipase-inhibition (71%) activities, moderate cytotoxic potential, and significant antibacterial activity. Gene expression of caspase in HepG2 cells was enhanced along with elevated production of ROS/RNS, while membrane integrity was disturbed upon the exposure of NPs. Overall results indicated that bio-assisted ZnO NPs exhibit excellent biological potential and could be exploited for future biomedical applications. particularly in antimicrobial and cancer therapeutics. Moreover, this is the first comprehensive study on Lepidium sativum-mediated synthesis of ZnO nanoparticles and evaluation of their biological activities. Full article

(This article belongs to the Special Issue Plant-Based Green Synthesis of Nanoparticles: Production, Characterization and Applications 2.0)

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15 pages, 4516 KiB

Open AccessArticle

Cannabidiol and Cannabigerol Inhibit Cholangiocarcinoma Growth In Vitro via Divergent Cell Death Pathways

by Michael J. Viereckl, Kelsey Krutsinger, Aaron Apawu, Jian Gu, Bryana Cardona, Donovan Barratt and Yuyan Han

Biomolecules 2022, 12(6), 854; https://doi.org/10.3390/biom12060854 - 20 Jun 2022

Cited by 17 | Viewed by 6620

Abstract

Cholangiocarcinoma (CCA) is a rare and highly lethal disease with few effective treatment options. Cannabinoids, cannabidiol (CBD) and cannabigerol (CBG) are non-psychedelic components extracted from cannabis. These non-psychoactive compounds have shown anti-proliferative potential in other tumor models; however, the efficacy of CBD and [...] Read more.

Cholangiocarcinoma (CCA) is a rare and highly lethal disease with few effective treatment options. Cannabinoids, cannabidiol (CBD) and cannabigerol (CBG) are non-psychedelic components extracted from cannabis. These non-psychoactive compounds have shown anti-proliferative potential in other tumor models; however, the efficacy of CBD and CBG in CCA is unknown. Furthermore, two cell death pathways are implicated with CBD resulting in autophagic degeneration and CBG in apoptosis. HuCC-T1 cells, Mz-ChA-1 cells (CCA cell lines) and H69 cells (immortalized cholangiocytes), were treated with CBD and CBG for 24 to 48 h. The influence of these cannabinoids on proliferation was assessed via MTT assay. Apoptosis and cell cycle were evaluated via Annexin-V apoptosis assay and propidium iodide, respectively. The expression of proliferation biomarker Ki-67, apoptosis biomarker BAX, and autophagic flux biomarkers LC3b and LAMP1 were evaluated via immunofluorescence. Cell migration and invasion were evaluated via wound healing assay and trans-well migration invasion assays, respectively. The colony formation was evaluated via colony formation assay. In addition, the expression of autophagy gene LC3b and apoptosis genes BAX, Bcl-2, and cleaved caspase-3 were evaluated via Western blot. CBD and CBG are non-selective anti-proliferative agents yielding similar growth curves in CCA; both cannabinoids are effective, yet CBG is more active at lower doses. Low doses of CBD and CBG enhanced immortalized cholangiocyte activity. The reduction in proliferation begins immediately and occurs maximally within 24 h of treatment. Moreover, a significant increase in the late-stage apoptosis and a reduction in the number of cells in S stage of the cell cycle indicates both CBD and CBG treatment could promote apoptosis and inhibit mitosis in CCA cells. The fluorescent expression of BAX and LC3b was significantly enhanced with CBD treatment when compared to control. LAMP1 and LC3b colocalization could also be observed with CBD and CBG treatment indicating changes in autophagic flux. A significant inhibition of migration, invasion and colony formation ability was shown in both CBD and CBG treatment in CCA. Western blot showed an overall decrease in the ratio of anti-apoptotic protein Bcl-2 with respect to pro-apoptotic protein BAX with CBG treatment. Furthermore, CBD treatment enhanced the expression of Type II cell death (autophagic degeneration) protein LC3b, which was reduced in CBG-treated CCA cells. Meanwhile, CBG treatment upregulated Type I cell death (programmed apoptosis) protein cleaved caspase-3. CBD and CBG are effective anti-cancer agents against CCA, capable of inhibiting the classic hallmarks of cancer, with a divergent mechanism of action (Type II or Type I respectively) in inducing these effects. Full article

(This article belongs to the Topic Non Herbal Nutraceutical, Probiotic, Vitamins and Fatty Acids in Cancer)

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16 pages, 4049 KiB

Open AccessEditor’s ChoiceArticle

Midazolam as a Probe for Heterotropic Drug-Drug Interactions Mediated by CYP3A4

by Ilia G. Denisov, Yelena V. Grinkova, Mark A. McLean, Tyler Camp and Stephen G. Sligar

Biomolecules 2022, 12(6), 853; https://doi.org/10.3390/biom12060853 - 20 Jun 2022

Cited by 9 | Viewed by 3133

Abstract

Human cytochrome P450 CYP3A4 is involved in the processing of more than 35% of current pharmaceuticals and therefore is responsible for multiple drug-drug interactions (DDI). In order to develop a method for the detection and prediction of the possible involvement of new drug [...] Read more.

Human cytochrome P450 CYP3A4 is involved in the processing of more than 35% of current pharmaceuticals and therefore is responsible for multiple drug-drug interactions (DDI). In order to develop a method for the detection and prediction of the possible involvement of new drug candidates in CYP3A4-mediated DDI, we evaluated the application of midazolam (MDZ) as a probe substrate. MDZ is hydroxylated by CYP3A4 in two positions: 1-hydroxy MDZ formed at lower substrate concentrations, and up to 35% of 4-hydroxy MDZ at high concentrations. The ratio of the formation rates of these two products (the site of metabolism ratio, SOM) was used as a measure of allosteric heterotropic interactions caused by effector molecules using CYP3A4 incorporated in lipid nanodiscs. The extent of the changes in the SOM in the presence of effectors is determined by chemical structure and is concentration-dependent. MD simulations of CYP3A4 in the lipid bilayer suggest that experimental results can be explained by the movement of the F-F’ loop and concomitant changes in the shape and volume of the substrate-binding pocket. As a result of PGS binding at the allosteric site, several residues directly contacting MDZ move away from the substrate molecule, enabling the repositioning of the latter for minor product formation. Full article

(This article belongs to the Special Issue New Insights into Cytochrome P450s)

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13 pages, 2329 KiB

Open AccessReview

The Benefits of Anthocyanins against Obesity-Induced Inflammation

by Chanya Ngamsamer, Jintana Sirivarasai and Nareerat Sutjarit

Biomolecules 2022, 12(6), 852; https://doi.org/10.3390/biom12060852 - 20 Jun 2022

Cited by 29 | Viewed by 5270

Abstract

Obesity has become a serious public health epidemic because of its associations with chronic conditions such as type 2 diabetes mellitus, hypertension, cardiovascular disease, and cancer. Obesity triggers inflammation marked by the secretion of low-grade inflammatory cytokines including interleukin-6, C-reactive protein, and tumor [...] Read more.

Obesity has become a serious public health epidemic because of its associations with chronic conditions such as type 2 diabetes mellitus, hypertension, cardiovascular disease, and cancer. Obesity triggers inflammation marked by the secretion of low-grade inflammatory cytokines including interleukin-6, C-reactive protein, and tumor necrosis factor-α, leading to a condition known as “meta-inflammation”. Currently, there is great interest in studying the treatment of obesity with food-derived bioactive compounds, which have low toxicity and no severe adverse events compared with pharmacotherapeutic agents. Here, we reviewed the beneficial effects of the bioactive compounds known as anthocyanins on obesity-induced inflammation. Foods rich in anthocyanins include tart cherries, red raspberries, black soybeans, blueberries, sweet cherries, strawberries and Queen Garnet plums. These anthocyanin-rich foods have been evaluated in cell culture, animal, and clinical studies, and found to be beneficial for health, reportedly reducing inflammatory markers. One factor in the development of obesity-related inflammation may be dysbiosis of the gut microbiome. Therefore, we focused this review on the in vitro and in vivo effects of anthocyanins on inflammation and the gut microbiota in obesity. Full article

(This article belongs to the Special Issue The Value of Natural Compounds as Therapeutic Agents)

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17 pages, 2302 KiB

Open AccessArticle

Neuroprotective Effects of Pharmacological Hypothermia on Hyperglycolysis and Gluconeogenesis in Rats after Ischemic Stroke

by Longfei Guan, Hangil Lee, Xiaokun Geng, Fengwu Li, Jiamei Shen, Yu Ji, Changya Peng, Huishan Du and Yuchuan Ding

Biomolecules 2022, 12(6), 851; https://doi.org/10.3390/biom12060851 - 19 Jun 2022

Cited by 13 | Viewed by 2994

Abstract

Stroke is a leading threat to human life. Metabolic dysfunction of glucose may play a key role in stroke pathophysiology. Pharmacological hypothermia (PH) is a potential neuroprotective strategy for stroke, in which the temperature is decreased safely. The present study determined whether neuroprotective [...] Read more.

Stroke is a leading threat to human life. Metabolic dysfunction of glucose may play a key role in stroke pathophysiology. Pharmacological hypothermia (PH) is a potential neuroprotective strategy for stroke, in which the temperature is decreased safely. The present study determined whether neuroprotective PH with chlorpromazine and promethazine (C + P), plus dihydrocapsaicin (DHC) improved glucose metabolism in acute ischemic stroke. A total of 208 adult male Sprague Dawley rats were randomly divided into the following groups: sham, stroke, and stroke with various treatments including C + P, DHC, C + P + DHC, phloretin (glucose transporter (GLUT)-1 inhibitor), cytochalasin B (GLUT-3 inhibitor), TZD (thiazolidinedione, phosphoenolpyruvate carboxykinase (PCK) inhibitor), and apocynin (nicotinamide adenine dinucleotide phosphate oxidase (NOX) inhibitor). Stroke was induced by middle cerebral artery occlusion (MCAO) for 2 h followed by 6 or 24 h of reperfusion. Rectal temperature was monitored before, during, and after PH. Infarct volume and neurological deficits were measured to assess the neuroprotective effects. Reactive oxygen species (ROS), NOX activity, lactate, apoptotic cell death, glucose, and ATP levels were measured. Protein expression of GLUT-1, GLUT-3, phosphofructokinase (PFK), lactate dehydrogenase (LDH), PCK1, PCK2, and NOX subunit gp91 was measured with Western blotting. PH with a combination of C + P and DHC induced faster, longer, and deeper hypothermia, as compared to each alone. PH significantly improved every measured outcome as compared to stroke and monotherapy. PH reduced brain infarction, neurological deficits, protein levels of glycolytic enzymes (GLUT-1, GLUT-3, PFK and LDH), gluconeogenic enzymes (PCK1 and PCK2), NOX activity and its subunit gp91, ROS, apoptotic cell death, glucose, and lactate, while raising ATP levels. In conclusion, stroke impaired glucose metabolism by enhancing hyperglycolysis and gluconeogenesis, which led to ischemic injury, all of which were reversed by PH induced by a combination of C + P and DHC. Full article

(This article belongs to the Special Issue Protection, Plasticity, and Physical Rehabilitation in Ischemic Injury)

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35 pages, 1396 KiB

Open AccessReview

Macrophages Are a Double-Edged Sword: Molecular Crosstalk between Tumor-Associated Macrophages and Cancer Stem Cells

by Shahang Luo, Guanghui Yang, Peng Ye, Nengqi Cao, Xiaoxia Chi, Wen-Hao Yang and Xiuwen Yan

Biomolecules 2022, 12(6), 850; https://doi.org/10.3390/biom12060850 - 19 Jun 2022

Cited by 24 | Viewed by 5050

Abstract

Cancer stem cells (CSCs) are a subset of highly tumorigenic cells in tumors. They have enhanced self-renewal properties, are usually chemo-radioresistant, and can promote tumor recurrence and metastasis. They can recruit macrophages into the tumor microenvironment and differentiate them into tumor-associated macrophages (TAMs). [...] Read more.

Cancer stem cells (CSCs) are a subset of highly tumorigenic cells in tumors. They have enhanced self-renewal properties, are usually chemo-radioresistant, and can promote tumor recurrence and metastasis. They can recruit macrophages into the tumor microenvironment and differentiate them into tumor-associated macrophages (TAMs). TAMs maintain CSC stemness and construct niches that are favorable for CSC survival. However, how CSCs and TAMs interact is not completely understood. An understanding on these mechanisms can provide additional targeting strategies for eliminating CSCs. In this review, we comprehensively summarize the reported mechanisms of crosstalk between CSCs and TAMs and update the related signaling pathways involved in tumor progression. In addition, we discuss potential therapies targeting CSC–TAM interaction, including targeting macrophage recruitment and polarization by CSCs and inhibiting the TAM-induced promotion of CSC stemness. This review also provides the perspective on the major challenge for developing potential therapeutic strategies to overcome CSC-TAM crosstalk. Full article

(This article belongs to the Special Issue Advances in Molecular Characterization and Therapeutic Targeting of Cancer Stem Cells)

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16 pages, 3331 KiB

Open AccessArticle

Excess Heme Promotes the Migration and Infiltration of Macrophages in Endometrial Hyperplasia Complicated with Abnormal Uterine Bleeding

by Lu-Yu Ruan, Zhen-Zhen Lai, Jia-Wei Shi, Hui-Li Yang, Jiang-Feng Ye, Feng Xie, Xue-Min Qiu, Xiao-Yong Zhu and Ming-Qing Li

Biomolecules 2022, 12(6), 849; https://doi.org/10.3390/biom12060849 - 19 Jun 2022

Cited by 7 | Viewed by 2501

Abstract

In patients, endometrial hyperplasia (EH) is often accompanied by abnormal uterine bleeding (AUB), which is prone to release large amounts of heme. However, the role of excess heme in the migration and infiltration of immune cells in EH complicated by AUB remains unknown. [...] Read more.

In patients, endometrial hyperplasia (EH) is often accompanied by abnormal uterine bleeding (AUB), which is prone to release large amounts of heme. However, the role of excess heme in the migration and infiltration of immune cells in EH complicated by AUB remains unknown. In this study, 45 patients with AUB were divided into three groups: a proliferative phase group (n = 15), a secretory phase group (n = 15) and EH (n = 15). We observed that immune cell subpopulations were significantly different among the three groups, as demonstrated by flow cytometry analysis. Of note, there was a higher infiltration of total immune cells and macrophages in the endometrium of patients with EH. Heme up-regulated the expression of heme oxygenase-1 (HO-1) and nuclear factor erythroid-2-related factor 2 (Nrf2) in endometrial epithelial cells (EECs) in vitro, as well as chemokine (e.g., CCL2, CCL3, CCL5, CXCL8) levels. Additionally, stimulation with heme led to the increased recruitment of THP-1 cells in an indirect EEC-THP-1 co-culture unit. These data suggest that sustained and excessive heme in patients with AUB may recruit macrophages by increasing the levels of several chemokines, contributing to the accumulation and infiltration of macrophages in the endometrium of EH patients, and the key molecules of heme metabolism, HO-1 and Nrf2, are also involved in this regulatory process. Full article

(This article belongs to the Special Issue Endocrine and Immune Metabolism Mechanisms in Endometrium-Related Diseases)

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19 pages, 3077 KiB

Open AccessArticle

Kir4.2 Potassium Channels in Retinal Pigment Epithelial Cells In Vitro: Contribution to Cell Viability and Proliferation, and Down-Regulation by Vascular Endothelial Growth Factor

by Marie-Christin Beer, Heidrun Kuhrt, Leon Kohen, Peter Wiedemann, Andreas Bringmann and Margrit Hollborn

Biomolecules 2022, 12(6), 848; https://doi.org/10.3390/biom12060848 - 18 Jun 2022

Viewed by 2399

Abstract

Dedifferentiation and proliferation of retinal pigment epithelial (RPE) cells are characteristics of retinal diseases. Dedifferentiation is likely associated with changes of inwardly rectifying potassium (Kir) channels. The roles of Kir4.2 channels in viability, and proliferation of cultured RPE cells were investigated. Gene expression [...] Read more.

Dedifferentiation and proliferation of retinal pigment epithelial (RPE) cells are characteristics of retinal diseases. Dedifferentiation is likely associated with changes of inwardly rectifying potassium (Kir) channels. The roles of Kir4.2 channels in viability, and proliferation of cultured RPE cells were investigated. Gene expression levels were determined using qRT-PCR. RPE cells expressed Kir2.1, 2.2, 2.4, 3.2, 4.1, 4.2, 6.1, and 7.1 mRNA. Kir4.2 protein was verified by immunocytochemistry and Western blotting. Kir4.2 mRNA in cultured cells was upregulated by hypoxia (hypoxia mimetic CoCl₂ or 0.2% O₂) and extracellular hyperosmolarity (addition of high NaCl or sucrose). Kir4.2 mRNA was suppressed by vascular endothelial growth factor (VEGF), blood serum, and thrombin whereas platelet-derived growth factor (PDGF), basic fibroblast growth factor (bFGF), and transforming growth factor-β1 (TGF-β1) increased it. Hyperosmotic Kir4.2 gene expression was mediated by TGF-β1 receptor signaling while hypoxic gene transcription was dependent on PDGF receptor signaling. VEGF receptor-2 blockade increased Kir4.2 mRNA level under control, hyperosmotic, and hypoxic conditions. SiRNA-mediated knockdown of Kir4.2 decreased the cell viability and proliferation under control and hyperosmotic conditions. Kir4.2 channels play functional roles in maintaining the viability and proliferation of RPE cells. Downregulation of Kir4.2 by VEGF, via activation of VEGF receptor-2 and induction of blood-retinal barrier breakdown, may contribute to decreased viability of RPE cells under pathological conditions. Full article

(This article belongs to the Special Issue Cell and Organ Cultures for Studying Retinal Diseases)

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11 pages, 812 KiB

Open AccessEditor’s ChoiceReview

CPLANE Complex and Ciliopathies

by Jesús Eduardo Martín-Salazar and Diana Valverde

Biomolecules 2022, 12(6), 847; https://doi.org/10.3390/biom12060847 - 17 Jun 2022

Cited by 12 | Viewed by 2724

Abstract

Primary cilia are non-motile organelles associated with the cell cycle, which can be found in most vertebrate cell types. Cilia formation occurs through a process called ciliogenesis, which involves several mechanisms including planar cell polarity (PCP) and the Hedgehog (Hh) signaling pathway. Some [...] Read more.

Primary cilia are non-motile organelles associated with the cell cycle, which can be found in most vertebrate cell types. Cilia formation occurs through a process called ciliogenesis, which involves several mechanisms including planar cell polarity (PCP) and the Hedgehog (Hh) signaling pathway. Some gene complexes, such as BBSome or CPLANE (ciliogenesis and planar polarity effector), have been linked to ciliogenesis. CPLANE complex is composed of INTU, FUZ and WDPCP, which bind to JBTS17 and RSG1 for cilia formation. Defects in these genes have been linked to a malfunction of intraflagellar transport and defects in the planar cell polarity, as well as defective activation of the Hedgehog signalling pathway. These faults lead to defective cilium formation, resulting in ciliopathies, including orofacial–digital syndrome (OFDS) and Bardet–Biedl syndrome (BBS). Considering the close relationship, between the CPLANE complex and cilium formation, it can be expected that defects in the genes that encode subunits of the CPLANE complex may be related to other ciliopathies. Full article

(This article belongs to the Special Issue Rare Diseases: From Molecular Pathways to Therapeutic Strategies)

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22 pages, 2587 KiB

Open AccessArticle

The Rheology and Printability of Cartilage Matrix-Only Biomaterials

by Emi A. Kiyotake, Michael E. Cheng, Emily E. Thomas and Michael S. Detamore

Biomolecules 2022, 12(6), 846; https://doi.org/10.3390/biom12060846 - 17 Jun 2022

Cited by 9 | Viewed by 2668

Abstract

The potential chondroinductivity from cartilage matrix makes it promising for cartilage repair; however, cartilage matrix-based hydrogels developed thus far have failed to match the mechanical performance of native cartilage or be bioprinted without adding polymers for reinforcement. There is a need for cartilage [...] Read more.

The potential chondroinductivity from cartilage matrix makes it promising for cartilage repair; however, cartilage matrix-based hydrogels developed thus far have failed to match the mechanical performance of native cartilage or be bioprinted without adding polymers for reinforcement. There is a need for cartilage matrix-based hydrogels with robust mechanical performance and paste-like precursor rheology for bioprinting/enhanced surgical placement. In the current study, our goals were to increase hydrogel stiffness and develop the paste-like precursor/printability of our methacryl-modified solubilized and devitalized cartilage (MeSDVC) hydrogels. We compared two methacryloylating reagents, methacrylic anhydride (MA) and glycidyl methacrylate (GM), and varied the molar excess (ME) of MA from 2 to 20. The MA-modified MeSDVCs had greater methacryloylation than GM-modified MeSDVC (20 ME). While GM and most of the MA hydrogel precursors exhibited paste-like rheology, the 2 ME MA and GM MeSDVCs had the best printability (i.e., shape fidelity, filament collapse). After crosslinking, the 2 ME MA MeSDVC had the highest stiffness (1.55 ± 0.23 MPa), approaching the modulus of native cartilage, and supported the viability/adhesion of seeded cells for 15 days. Overall, the MA (2 ME) improved methacryloylation, hydrogel stiffness, and printability, resulting in a stand-alone MeSDVC printable biomaterial. The MeSDVC has potential as a future bioink and has future clinical relevance for cartilage repair. Full article

(This article belongs to the Special Issue Extracellular Matrix-Based Bioinks for 3D Bioprinting Applications)

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10 pages, 1747 KiB

Open AccessReview

Genomic Variation-Mediating Fluconazole Resistance in Yeast

by Wen-Yao Wang, Hong-Qing Cai, Si-Yuan Qu, Wei-Hao Lin, Cheng-Cheng Liang, Hao Liu, Ze-Xiong Xie and Ying-Jin Yuan

Biomolecules 2022, 12(6), 845; https://doi.org/10.3390/biom12060845 - 17 Jun 2022

Cited by 6 | Viewed by 3010

Abstract

Fungal infections pose a serious and growing threat to public health. These infections can be treated with antifungal drugs by killing hazardous fungi in the body. However, the resistance can develop over time when fungi are exposed to antifungal drugs by generating genomic [...] Read more.

Fungal infections pose a serious and growing threat to public health. These infections can be treated with antifungal drugs by killing hazardous fungi in the body. However, the resistance can develop over time when fungi are exposed to antifungal drugs by generating genomic variations, including mutation, aneuploidy, and loss of heterozygosity. The variations could reduce the binding affinity of a drug to its target or block the pathway through which drugs exert their activity. Here, we review genomic variation-mediating fluconazole resistance in the yeast Candida, with the hope of highlighting the functional consequences of genomic variations for the antifungal resistance. Full article

(This article belongs to the Special Issue Theme Issue Honoring Scientist Louis Pasteur on His 200th Birthday)

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13 pages, 655 KiB

Open AccessArticle

Alkaloids of Dicranostigma franchetianum (Papaveraceae) and Berberine Derivatives as a New Class of Antimycobacterial Agents

by Viriyanata Wijaya, Ondřej Janďourek, Jana Křoustková, Kateřina Hradiská-Breiterová, Jan Korábečný, Kateřina Sobolová, Eliška Kohelová, Anna Hošťálková, Klára Konečná, Marcela Šafratová, Rudolf Vrabec, Jiří Kuneš, Lubomír Opletal, Jakub Chlebek and Lucie Cahlíková

Biomolecules 2022, 12(6), 844; https://doi.org/10.3390/biom12060844 - 17 Jun 2022

Cited by 7 | Viewed by 2689

Abstract

Tuberculosis (TB) is a widespread infectious disease caused by Mycobacterium tuberculosis. The increasing incidence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains has created a need for new antiTB agents with new chemical scaffolds to combat the disease. Thus, the key question [...] Read more.

Tuberculosis (TB) is a widespread infectious disease caused by Mycobacterium tuberculosis. The increasing incidence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains has created a need for new antiTB agents with new chemical scaffolds to combat the disease. Thus, the key question is: how to search for new antiTB and where to look for them? One of the possibilities is to search among natural products (NPs). In order to search for new antiTB drugs, the detailed phytochemical study of the whole Dicranostigma franchetianum plant was performed isolating wide spectrum of isoquinoline alkaloids (IAs). The chemical structures of the isolated alkaloids were determined by a combination of MS, HRMS, 1D, and 2D NMR techniques, and by comparison with literature data. Alkaloids were screened against Mycobacterium tuberculosis H37Ra and four other mycobacterial strains (M. aurum, M. avium, M. kansasii, and M. smegmatis). Alkaloids 3 and 5 showed moderate antimycobacterial activity against all tested strains (MICs 15.625–31.25 µg/mL). Furthermore, ten semisynthetic berberine (16a–16k) derivatives were developed and tested for antimycobacterial activity. In general, the derivatization of berberine was connected with a significant increase in antimycobacterial activity against all tested strains (MICs 0.39–7.81 μg/mL). Two derivatives (16e, 16k) were identified as compounds with micromolar MICs against M. tuberculosis H37Ra (MIC 2.96 and 2.78 µM). All compounds were also evaluated for their in vitro hepatotoxicity on a hepatocellular carcinoma cell line (HepG2), exerting lower cytotoxicity profile than their MIC values, thereby potentially reaching an effective concentration without revealing toxic side effects. Full article

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

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14 pages, 2356 KiB

Open AccessEditor’s ChoiceArticle

Growth-Suppressive and Apoptosis-Inducing Effects of Tetrandrine in SW872 Human Malignant Liposarcoma Cells via Activation of Caspase-9, Down-Regulation of XIAP and STAT-3, and ER Stress

by Mohammed Samsuzzaman and Byeong-Churl Jang

Biomolecules 2022, 12(6), 843; https://doi.org/10.3390/biom12060843 - 17 Jun 2022

Cited by 5 | Viewed by 2278

Abstract

Liposarcoma is a rare and heterogeneous soft tissue malignant tumor and has a significant impact on mortality with a poor prognosis. To date, there is no effective treatment for liposarcoma, whereas surgical resection is only the gold treatment with numerous adverse effects. Here [...] Read more.

Liposarcoma is a rare and heterogeneous soft tissue malignant tumor and has a significant impact on mortality with a poor prognosis. To date, there is no effective treatment for liposarcoma, whereas surgical resection is only the gold treatment with numerous adverse effects. Here we investigated whether tetrandrine inhibits the growth of SW872 human malignant liposarcoma cells. Of note, tetrandrine at 10 μM vastly inhibited growth and induced apoptosis, as evidenced by increased nuclear DNA fragmentation and sub-G1 population of SW872 cells. Mechanistically, treatment with tetrandrine led to activation of caspase-9/3 in SW872 cells, and z-VAD-fmk, a pan-caspase inhibitor, attenuated the tetrandrine-induced apoptosis and growth suppression in SW872 cells. In addition, tetrandrine treatment resulted in down-regulation of XIAP andSTAT-3 in SW872 cells, and importantly knockdown of STAT-3 caused a significant reduction of the cell survival. Tetrandrine also had abilities to up-regulate not only the expression of GRP78 and ATF-4 but also the phosphorylation of eIF-2α in SW872 cells. In summary, these results demonstrated that tetrandrine has strong growth-suppressive and apoptosis-inducing effects on SW872 cells, which are mediated through control of the intrinsic caspase pathway, down-regulation of XIAP and STAT-3, and triggering ER stress. Full article

(This article belongs to the Collection Feature Papers in Chemical Biology)

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17 pages, 2872 KiB

Open AccessArticle

Influence of Inhibition of COX-2-Dependent Lipid Metabolism on Regulation of UVB-Induced Keratinocytes Apoptosis by Cannabinoids

by Piotr Wójcik, Michał Biernacki, Natalia Domian, Neven Žarković and Elżbieta Skrzydlewska

Biomolecules 2022, 12(6), 842; https://doi.org/10.3390/biom12060842 - 17 Jun 2022

Cited by 6 | Viewed by 2749

Abstract

Inflammation and apoptosis are regulated by similar factors, including ultraviolet B (UVB) radiation and cannabinoids, which are metabolized by cyclooxygenase-2 (COX-2) into pro-apoptotic prostaglandin derivatives. Thus, the aim of this study was to evaluate the impact of cyclooxygenase-2 inhibition by celecoxib on the [...] Read more.

Inflammation and apoptosis are regulated by similar factors, including ultraviolet B (UVB) radiation and cannabinoids, which are metabolized by cyclooxygenase-2 (COX-2) into pro-apoptotic prostaglandin derivatives. Thus, the aim of this study was to evaluate the impact of cyclooxygenase-2 inhibition by celecoxib on the apoptosis of keratinocytes modulated by UVB, anandamide (AEA) and cannabidiol (CBD). For this purpose, keratinocytes were non-treated/treated with celecoxib and/or with UVB and CBD and AEA. Apoptosis was evaluated using microscopy, gene expressions using quantitate reverse-transcriptase polymerase chain reaction; prostaglandins using liquid chromatography tandem mass spectrometry and cyclooxygenase activity using spectrophotometry. UVB enhances the percentage of apoptotic keratinocytes, which can be caused by the increased prostaglandin generation by cyclooxygenase-2, or/and induced cannabinoid receptor 1/2 (CB1/2) expression. AEA used alone intensifies apoptosis by affecting caspase expression, and in UVB-irradiated keratinocytes, cyclooxygenase-2 activity is increased, while CBD acts as a cytoprotective when used with or without UVB. After COX-2 inhibition, UVB-induced changes are partially ameliorated, when anandamide becomes an anti-apoptotic agent. It can be caused by observed reduced generation of anandamide pro-apoptotic derivative prostaglandin-ethanolamide by COX. Therefore, products of cyclooxygenase-dependent lipid metabolism seem to play an important role in the modulation of UVB-induced apoptosis by cannabinoids, which is particularly significant in case of AEA as inhibition of cyclooxygenase reduces the generation of pro-apoptotic lipid mediators and thus prevents apoptosis. Full article

(This article belongs to the Special Issue Lipid Metabolism in Health and Disease)

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12 pages, 1129 KiB

Open AccessArticle

Automated Protein Secondary Structure Assignment from Cα Positions Using Neural Networks

by Mohammad N. Saqib, Justyna D. Kryś and Dominik Gront

Biomolecules 2022, 12(6), 841; https://doi.org/10.3390/biom12060841 - 17 Jun 2022

Cited by 2 | Viewed by 2645

Abstract

The assignment of secondary structure elements in protein conformations is necessary to interpret a protein model that has been established by computational methods. The process essentially involves labeling the amino acid residues with H (Helix), E (Strand), or C (Coil, also known as [...] Read more.

The assignment of secondary structure elements in protein conformations is necessary to interpret a protein model that has been established by computational methods. The process essentially involves labeling the amino acid residues with H (Helix), E (Strand), or C (Coil, also known as Loop). When particular atoms are absent from an input protein structure, the procedure becomes more complicated, especially when only the alpha carbon locations are known. Various techniques have been tested and applied to this problem during the last forty years. The application of machine learning techniques is the most recent trend. This contribution presents the HECA classifier, which uses neural networks to assign protein secondary structure types. The technique exclusively employs C

α

coordinates. The Keras (TensorFlow) library was used to implement and train the neural network model. The BioShell toolkit was used to calculate the neural network input features from raw coordinates. The study’s findings show that neural network-based methods may be successfully used to take on structure assignment challenges when only C

α

trace is available. Thanks to the careful selection of input features, our approach’s accuracy (above 97%) exceeded that of the existing methods. Full article

(This article belongs to the Collection Feature Papers in Bioinformatics and Systems Biology Section)

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36 pages, 1264 KiB

Open AccessReview

Role of Seipin in Human Diseases and Experimental Animal Models

by Yuying Li, Xinmin Yang, Linrui Peng, Qing Xia, Yuwei Zhang, Wei Huang, Tingting Liu and Da Jia

Biomolecules 2022, 12(6), 840; https://doi.org/10.3390/biom12060840 - 17 Jun 2022

Cited by 9 | Viewed by 3876

Abstract

Seipin, a protein encoded by the Berardinelli-Seip congenital lipodystrophy type 2 (BSCL2) gene, is famous for its key role in the biogenesis of lipid droplets and type 2 congenital generalised lipodystrophy (CGL2). BSCL2 gene mutations result in genetic diseases including CGL2, [...] Read more.

Seipin, a protein encoded by the Berardinelli-Seip congenital lipodystrophy type 2 (BSCL2) gene, is famous for its key role in the biogenesis of lipid droplets and type 2 congenital generalised lipodystrophy (CGL2). BSCL2 gene mutations result in genetic diseases including CGL2, progressive encephalopathy with or without lipodystrophy (also called Celia’s encephalopathy), and BSCL2-associated motor neuron diseases. Abnormal expression of seipin has also been found in hepatic steatosis, neurodegenerative diseases, glioblastoma stroke, cardiac hypertrophy, and other diseases. In the current study, we comprehensively summarise phenotypes, underlying mechanisms, and treatment of human diseases caused by BSCL2 gene mutations, paralleled by animal studies including systemic or specific Bscl2 gene knockout, or Bscl2 gene overexpression. In various animal models representing diseases that are not related to Bscl2 mutations, differential expression patterns and functional roles of seipin are also described. Furthermore, we highlight the potential therapeutic approaches by targeting seipin or its upstream and downstream signalling pathways. Taken together, restoring adipose tissue function and targeting seipin-related pathways are effective strategies for CGL2 treatment. Meanwhile, seipin-related pathways are also considered to have potential therapeutic value in diseases that are not caused by BSCL2 gene mutations. Full article

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18 pages, 2426 KiB

Open AccessArticle

Grape-Seed Procyanidin Extract (GSPE) Seasonal-Dependent Modulation of Glucose and Lipid Metabolism in the Liver of Healthy F344 Rats

by Romina M. Rodríguez, Marina Colom-Pellicer, Jordi Blanco, Enrique Calvo, Gerard Aragonès and Miquel Mulero

Biomolecules 2022, 12(6), 839; https://doi.org/10.3390/biom12060839 - 17 Jun 2022

Cited by 9 | Viewed by 2925

Abstract

Seasonality is gaining attention in the modulation of some physiological and metabolic functions in mammals. Furthermore, the consumption of natural compounds, such as GSPE, is steadily increasing. Consequently, in order to study the interaction of seasonal variations in day length over natural compounds’ [...] Read more.

Seasonality is gaining attention in the modulation of some physiological and metabolic functions in mammals. Furthermore, the consumption of natural compounds, such as GSPE, is steadily increasing. Consequently, in order to study the interaction of seasonal variations in day length over natural compounds’ molecular effects, we carried out an animal study using photo-sensitive rats which were chronically exposed for 9 weeks to three photoperiods (L6, L18, and L12) in order to mimic the day length of different seasons (winter/summer/and autumn-spring). In parallel, animals were also treated either with GSPE 25 (mg/kg) or vehicle (VH) for 4 weeks. Interestingly, a seasonal-dependent GSPE modulation on the hepatic glucose and lipid metabolism was observed. For example, some metabolic genes from the liver (SREBP-1c, Gk, Acacα) changed their expression due to seasonality. Furthermore, the metabolomic results also indicated a seasonal influence on the GSPE effects associated with glucose-6-phosphate, D-glucose, and D-ribose, among others. These differential effects, which were also reflected in some plasmatic parameters (i.e., glucose and triglycerides) and hormones (corticosterone and melatonin), were also associated with significant changes in the expression of several hepatic circadian clock genes (Bmal1, Cry1, and Nr1d1) and ER stress genes (Atf6, Grp78, and Chop). Our results point out the importance of circannual rhythms in regulating metabolic homeostasis and suggest that seasonal variations (long or short photoperiods) affect hepatic metabolism in rats. Furthermore, they suggest that procyanidin consumption could be useful for the modulation of the photoperiod-dependent changes on glucose and lipid metabolism, whose alterations could be related to metabolic diseases (e.g., diabetes, obesity, and cardiovascular disease). Furthermore, even though the GSPE effect is not restricted to a specific photoperiod, our results suggest a more significant effect in the L18 condition. Full article

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16 pages, 7883 KiB

Open AccessArticle

Effects of Hypoxia on Proliferation and Differentiation in Belgian Blue and Hanwoo Muscle Satellite Cells for the Development of Cultured Meat

by Sanghun Park, Mick Gagliardi, Geertje Swennen, Arin Dogan, Yuna Kim, Yunhwan Park, Gyutae Park, Sehyuk Oh, Mark Post and Jungseok Choi

Biomolecules 2022, 12(6), 838; https://doi.org/10.3390/biom12060838 - 16 Jun 2022

Cited by 11 | Viewed by 4141

Abstract

Among future food problems, the demand for meat is expected to increase rapidly, but the production efficiency of meat, which is a protein source, is very low compared to other foods. To address this problem, research on the development and production of cultured [...] Read more.

Among future food problems, the demand for meat is expected to increase rapidly, but the production efficiency of meat, which is a protein source, is very low compared to other foods. To address this problem, research on the development and production of cultured meat as an alternative meat source using muscle stem cells in vitro has recently been undertaken. Many studies have been conducted on myosatellite cells for medical purposes, but studies on alternative meat production are rare. In vitro cell culture mimics the in vivo environment for cell growth. The satellite cell niche is closer to hypoxic (2% O₂) than normoxic (20% O₂) conditions. The aim of this study was to investigate the efficient oxygen conditions of myosatellite cell cultures for the production of cultured meat. The bovine satellite cell counts and mRNA (Pax7, Myf5 and HIF1α) levels were higher in hypoxia than normoxia (p < 0.05). Through Hoechst-positive nuclei counts, and expression of Pax7, MyoD and myosin protein by immunofluorescence, it was confirmed that muscle cells performed normal proliferation and differentiation. Myoblast fusion was higher under hypoxic conditions (p < 0.05), and the myotube diameters were also thicker (p < 0.05). In the myotube, the number of cells was high in hypoxia, and the expression of the total protein amounts, differentiation marker mRNA (myogenin, myosin and TOM20), and protein markers (myosin and TOM20) was also high. The study results demonstrated that the proliferation and differentiation of bovine myosatellite cells were promoted more highly under hypoxic conditions than under normoxic conditions. Therefore, hypoxic cultures that promote the proliferation and differentiation of bovine myosatellite cells may be an important factor in the development of cultured meat. Full article

(This article belongs to the Special Issue Physiological Cell Culture)

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16 pages, 3712 KiB

Open AccessArticle

Multi-Scale Analysis of the Composition, Structure, and Function of Decellularized Extracellular Matrix for Human Skin and Wound Healing Models

by Atiya M. Sarmin, Nadia El Moussaid, Ratima Suntornnond, Eleanor J. Tyler, Yang-Hee Kim, Stefania Di Cio, William V. Megone, Oliver Pearce, Julien E. Gautrot, Jonathan Dawson and John T. Connelly

Biomolecules 2022, 12(6), 837; https://doi.org/10.3390/biom12060837 - 16 Jun 2022

Cited by 17 | Viewed by 4572

Abstract

The extracellular matrix (ECM) is a complex mixture of structural proteins, proteoglycans, and signaling molecules that are essential for tissue integrity and homeostasis. While a number of recent studies have explored the use of decellularized ECM (dECM) as a biomaterial for tissue engineering, [...] Read more.

The extracellular matrix (ECM) is a complex mixture of structural proteins, proteoglycans, and signaling molecules that are essential for tissue integrity and homeostasis. While a number of recent studies have explored the use of decellularized ECM (dECM) as a biomaterial for tissue engineering, the complete composition, structure, and mechanics of these materials remain incompletely understood. In this study, we performed an in-depth characterization of skin-derived dECM biomaterials for human skin equivalent (HSE) models. The dECM materials were purified from porcine skin, and through mass spectrometry profiling, we quantified the presence of major ECM molecules, including types I, III, and VI collagen, fibrillin, and lumican. Rheological analysis demonstrated the sol-gel and shear-thinning properties of dECM materials, indicating their physical suitability as a tissue scaffold, while electron microscopy revealed a complex, hierarchical structure of nanofibers in dECM hydrogels. The dECM materials were compatible with advanced biofabrication techniques, including 3D printing within a gelatin microparticle support bath, printing with a sacrificial material, or blending with other ECM molecules to achieve more complex compositions and structures. As a proof of concept, we also demonstrate how dECM materials can be fabricated into a 3D skin wound healing model using 3D printing. Skin-derived dECM therefore represents a complex and versatile biomaterial with advantageous properties for the fabrication of next-generation HSEs. Full article

(This article belongs to the Special Issue Extracellular Matrix-Based Bioinks for 3D Bioprinting Applications)

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11 pages, 1199 KiB

Open AccessArticle

Alternative c-MYC mRNA Transcripts as an Additional Tool for c-Myc2 and c-MycS Production in BL60 Tumors

by Dina Ibrahim, Léa Prévaud, Nathalie Faumont, Danielle Troutaud, Jean Feuillard, Mona Diab-Assaf and Ahmad Oulmouden

Biomolecules 2022, 12(6), 836; https://doi.org/10.3390/biom12060836 - 16 Jun 2022

Cited by 2 | Viewed by 3009

Abstract

While studying c-Myc protein expression in several Burkitt lymphoma cell lines and in lymph nodes from a mouse model bearing a translocated c-MYC gene from the human BL line IARC-BL60, we surprisingly discovered a complex electrophoretic profile. Indeed, the BL60 cell line carrying [...] Read more.

While studying c-Myc protein expression in several Burkitt lymphoma cell lines and in lymph nodes from a mouse model bearing a translocated c-MYC gene from the human BL line IARC-BL60, we surprisingly discovered a complex electrophoretic profile. Indeed, the BL60 cell line carrying the t(8;22) c-MYC translocation exhibits a simple pattern, with a single c-Myc2 isoform. Analysis of the c-MYC transcripts expressed by tumor lymph nodes in the mouse λc-MYC (A^vy/a) showed for the first time five transcripts that are associated with t(8;22) c-MYC translocation. The five transcripts were correlated with the production of c-Myc2 and c-MycS, and loss of c-Myc1. The contribution of these transcripts to the oncogenic activation of the t(8;22) c-MYC is discussed. Full article

(This article belongs to the Special Issue Lymphoma: From Molecular Biology to Targeted Therapy)

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16 pages, 3673 KiB

Open AccessArticle

A Novel Antiviral Protein Derived from Oenanthe javanica: Type I Interferon-Dependent Antiviral Signaling and Its Pharmacological Potential

by Bo-Ram Jo, Hyun-Soo Kim, Jeong-Won Ahn, Eui-Young Jeoung, Su-Kil Jang, Yeong-Min Yoo and Seong-Soo Joo

Biomolecules 2022, 12(6), 835; https://doi.org/10.3390/biom12060835 - 16 Jun 2022

Cited by 3 | Viewed by 2246

Abstract

Pathogenesis-related (PR) proteins produced in plants play a crucial role in self-defense against microbial attacks. Previously, we have identified a novel PR-1-like protein (OPRP) from Oenanthe javanica and examined its pharmacologic relevance and cell signaling in mammalian cells. Purified full-length OPRP protein significantly [...] Read more.

Pathogenesis-related (PR) proteins produced in plants play a crucial role in self-defense against microbial attacks. Previously, we have identified a novel PR-1-like protein (OPRP) from Oenanthe javanica and examined its pharmacologic relevance and cell signaling in mammalian cells. Purified full-length OPRP protein significantly increased toll-like receptor 4 (TLR4)-dependent expression levels of genes such as inducible nitric oxide synthase (iNOS), tumor necrosis factor α (TNF-α), interleukin 6 (IL-6), and CD80. We also found that small peptides (OPRP2 and OPRP3) designed from OPRP remarkably upregulated myxovirus resistance (Mx1), 2′-5′ oligoadenylate sythetase (OAS), and interferon (IFN) α/β genes in mouse splenocytes as well as human epithelial cells. Notably, OPRP protein distinctively activated STAT1 phosphorylation and ISGF-3γ. Interestingly, OPRP2 and OPRP3 were internalized to the cytoplasm and triggered dimerization of STAT1/STAT2, followed by upregulation of type I IFN-dependent antiviral cytokines. Moreover, OPRP1 successfully inhibited viral (Pseudo SARS-CoV-2) entry into host cells. Taken together, we conclude that OPRP and its small peptides (OPRP1 to 3) present a new therapeutic intervention for modulating innate immune activity through type I IFN-dependent antiviral signaling and a new therapeutic approach that drives an antiviral state in non-immune cells by producing antiviral cytokines. Full article

(This article belongs to the Topic Novel Biomolecules Modulating Innate Immune Responses against Virus Infection)

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26 pages, 3750 KiB

Open AccessArticle

Optimization and Characterization of a Novel Exopolysaccharide from Bacillus haynesii CamB6 for Food Applications

by Aparna Banerjee, Sura Jasem Mohammed Breig, Aleydis Gómez, Ignacio Sánchez-Arévalo, Patricio González-Faune, Shrabana Sarkar, Rajib Bandopadhyay, Sugunakar Vuree, Jorge Cornejo, Jaime Tapia, Gaston Bravo and Gustavo Cabrera-Barjas

Biomolecules 2022, 12(6), 834; https://doi.org/10.3390/biom12060834 - 15 Jun 2022

Cited by 31 | Viewed by 5151

Abstract

Extremophilic microorganisms often produce novel bioactive compounds to survive under harsh environmental conditions. Exopolysaccharides (EPSs), a constitutive part of bacterial biofilm, are functional biopolymers that act as a protecting sheath to the extremophilic bacteria and are of high industrial value. In this study, [...] Read more.

Extremophilic microorganisms often produce novel bioactive compounds to survive under harsh environmental conditions. Exopolysaccharides (EPSs), a constitutive part of bacterial biofilm, are functional biopolymers that act as a protecting sheath to the extremophilic bacteria and are of high industrial value. In this study, we elucidate a new EPS produced by thermophilic Bacillus haynesii CamB6 from a slightly acidic (pH 5.82) Campanario hot spring (56.4 °C) located in the Central Andean Mountains of Chile. Physicochemical properties of the EPS were characterized by different techniques: Scanning electron microscopy- energy dispersive X-ray spectroscopy (SEM-EDS), Atomic Force Microscopy (AFM), High-Performance Liquid Chromatography (HPLC), Gel permeation chromatography (GPC), Fourier Transform Infrared Spectroscopy (FTIR), 1D and 2D Nuclear Magnetic Resonance (NMR), and Thermogravimetric analysis (TGA). The EPS demonstrated amorphous surface roughness composed of evenly distributed macromolecular lumps. GPC and HPLC analysis showed that the EPS is a low molecular weight heteropolymer composed of mannose (66%), glucose (20%), and galactose (14%). FTIR analysis demonstrated the polysaccharide nature (–OH groups, Acetyl groups, and pyranosic ring structure) and the presence of different glycosidic linkages among sugar residues, which was further confirmed by NMR spectroscopic analyses. Moreover, D-mannose α-(1→2) and α-(1→4) linkages prevail in the CamB6 EPS structure. TGA revealed the high thermal stability (240 °C) of the polysaccharide. The functional properties of the EPS were evaluated for food industry applications, specifically as an antioxidant and for its emulsification, water-holding (WHC), oil-holding (OHC), and flocculation capacities. The results suggest that the study EPS can be a useful additive for the food-processing industry. Full article

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16 pages, 580 KiB

Open AccessArticle

Association between Vitamin D Receptor Gene Polymorphisms and Periodontal Bacteria: A Clinical Pilot Study

by Concetta Cafiero, Cristina Grippaudo, Marco Dell’Aquila, Pasquale Cimmino, Antonio D’Addona, Paolo De Angelis, Maria Pia Ottaiano, Domenico Costagliola, Giulio Benincasa, Alessandra Micera, Luigi Santacroce and Raffaele Palmirotta

Biomolecules 2022, 12(6), 833; https://doi.org/10.3390/biom12060833 - 15 Jun 2022

Cited by 5 | Viewed by 2636

Abstract

Background: Periodontitis is an inflammatory disease caused by microorganisms involving the supporting tissues of the teeth. Gene variants may influence both the composition of the biofilm in the oral cavity and the host response. The objective of the study was to investigate the [...] Read more.

Background: Periodontitis is an inflammatory disease caused by microorganisms involving the supporting tissues of the teeth. Gene variants may influence both the composition of the biofilm in the oral cavity and the host response. The objective of the study was to investigate the potential correlations between the disease susceptibility, the presence and the quantity of periodontopathogenic oral bacterial composition and the VDR gene polymorphisms. Methods: Fifty (50) unrelated periodontal patients and forty-one (41) healthy controls were selected for genomic DNA extraction. DNA concentration was measured and analyzed. The periodontopathogenic bacterial species were identified and quantified using a Real Time PCR performed with species-specific primers and probes. Results: Genotype distribution showed a different distribution between the groups for BsmI rs1544410 genotypes (p = 0.0001) with a prevalence of the G(b) allele in periodontal patients (p = 0.0003). Statistical significance was also found for VDR TaqI rs731236 (p ≤ 0.00001) with a prevalence of the T(T) allele in periodontal patients (p ≤ 0.00001). The average bacterial copy count for the periodontitis group was significantly higher than that of control group. Dividing patients into two groups based on high or low bacterial load, FokI rs2228570 T allele (f) was statistically more represented in patients with high bacterial load. Conclusions: The findings of the study suggest the involvement of the VDR gene BsmI and TaqI polymorphisms in periodontal disease, while FokI and BsmI may be involved in determining an increased presence of periodontopathogens. Full article

(This article belongs to the Section Biological and Bio- Materials)

24 pages, 4142 KiB

Open AccessEditor’s ChoiceArticle

Non-Equilibrium Protein Folding and Activation by ATP-Driven Chaperones

by Huafeng Xu

Biomolecules 2022, 12(6), 832; https://doi.org/10.3390/biom12060832 - 15 Jun 2022

Cited by 3 | Viewed by 3889

Abstract

Recent experimental studies suggest that ATP-driven molecular chaperones can stabilize protein substrates in their native structures out of thermal equilibrium. The mechanism of such non-equilibrium protein folding is an open question. Based on available structural and biochemical evidence, I propose here a unifying [...] Read more.

Recent experimental studies suggest that ATP-driven molecular chaperones can stabilize protein substrates in their native structures out of thermal equilibrium. The mechanism of such non-equilibrium protein folding is an open question. Based on available structural and biochemical evidence, I propose here a unifying principle that underlies the conversion of chemical energy from ATP hydrolysis to the conformational free energy associated with protein folding and activation. I demonstrate that non-equilibrium folding requires the chaperones to break at least one of four symmetry conditions. The Hsp70 and Hsp90 chaperones each break a different subset of these symmetries and thus they use different mechanisms for non-equilibrium protein folding. I derive an upper bound on the non-equilibrium elevation of the native concentration, which implies that non-equilibrium folding only occurs in slow-folding proteins that adopt an unstable intermediate conformation in binding to ATP-driven chaperones. Contrary to the long-held view of Anfinsen’s hypothesis that proteins fold to their conformational free energy minima, my results predict that some proteins may fold into thermodynamically unstable native structures with the assistance of ATP-driven chaperones, and that the native structures of some chaperone-dependent proteins may be shaped by their chaperone-mediated folding pathways. Full article

(This article belongs to the Special Issue Hsp90 Structure, Mechanism and Disease)

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20 pages, 1457 KiB

Open AccessReview

Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization—A Timing Chain for the Bacterial Growth Cycle?

by Georgi Muskhelishvili, Patrick Sobetzko and Andrew Travers

Biomolecules 2022, 12(6), 831; https://doi.org/10.3390/biom12060831 - 15 Jun 2022

Cited by 3 | Viewed by 2583

Abstract

In this article we describe the bacterial growth cycle as a closed, self-reproducing, or autopoietic circuit, reestablishing the physiological state of stationary cells initially inoculated in the growth medium. In batch culture, this process of self-reproduction is associated with the gradual decline in [...] Read more.

In this article we describe the bacterial growth cycle as a closed, self-reproducing, or autopoietic circuit, reestablishing the physiological state of stationary cells initially inoculated in the growth medium. In batch culture, this process of self-reproduction is associated with the gradual decline in available metabolic energy and corresponding change in the physiological state of the population as a function of “travelled distance” along the autopoietic path. We argue that this directional alteration of cell physiology is both reflected in and supported by sequential gene expression along the chromosomal OriC-Ter axis. We propose that during the E. coli growth cycle, the spatiotemporal order of gene expression is established by coupling the temporal gradient of supercoiling energy to the spatial gradient of DNA thermodynamic stability along the chromosomal OriC-Ter axis. Full article

(This article belongs to the Collection Feature Papers in Molecular Genetics)

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16 pages, 3725 KiB

Open AccessEditor’s ChoiceArticle

Selective Upregulation of SIRT1 Expression in Retinal Ganglion Cells by AAV-Mediated Gene Delivery Increases Neuronal Cell Survival and Alleviates Axon Demyelination Associated with Optic Neuritis

by Ahmara G. Ross, Brahim Chaqour, Devin S. McDougald, Kimberly E. Dine, Thu T. Duong, Ryan E. Shindler, Jipeng Yue, Tehui Liu and Kenneth S. Shindler

Biomolecules 2022, 12(6), 830; https://doi.org/10.3390/biom12060830 - 14 Jun 2022

Cited by 15 | Viewed by 3589

Abstract

Optic neuritis (ON), the most common ocular manifestation of multiple sclerosis, is an autoimmune inflammatory demyelinating disease also characterized by degeneration of retinal ganglion cells (RGCs) and their axons, which commonly leads to visual impairment despite attempted treatments. Although ON disease etiology is [...] Read more.

Optic neuritis (ON), the most common ocular manifestation of multiple sclerosis, is an autoimmune inflammatory demyelinating disease also characterized by degeneration of retinal ganglion cells (RGCs) and their axons, which commonly leads to visual impairment despite attempted treatments. Although ON disease etiology is not known, changes in the redox system and exacerbated optic nerve inflammation play a major role in the pathogenesis of the disease. Silent information regulator 1 (sirtuin-1/SIRT1) is a ubiquitously expressed NAD⁺-dependent deacetylase, which functions to reduce/prevent both oxidative stress and inflammation in various tissues. Non-specific upregulation of SIRT1 by pharmacologic and genetic approaches attenuates RGC loss in experimental ON. Herein, we hypothesized that targeted expression of SIRT1 selectively in RGCs using an adeno-associated virus (AAV) vector as a delivery vehicle is an effective approach to reducing neurodegeneration and preserving vision in ON. We tested this hypothesis through intravitreal injection of AAV7m8.SNCG.SIRT1, an AAV2-derived vector optimized for highly efficient SIRT1 transgene transfer and protein expression into RGCs in mice with experimental autoimmune encephalomyelitis (EAE), a model of multiple sclerosis that recapitulates optic neuritis RGC loss and axon demyelination. Our data show that EAE mice injected with a control vehicle exhibit progressive alteration of visual function reflected by decreasing optokinetic response (OKR) scores, whereas comparatively, AAV7m8.SNCG.SIRT1-injected EAE mice maintain higher OKR scores, suggesting that SIRT1 reduces the visual deficit imparted by EAE. Consistent with this, RGC survival determined by immunolabeling is increased and axon demyelination is decreased in the AAV7m8.SNCG.SIRT1 RGC-injected group of EAE mice compared to the mouse EAE counterpart injected with a vehicle or with control vector AAV7m8.SNCG.eGFP. However, immune cell infiltration of the optic nerve is not significantly different among all EAE groups of mice injected with either vehicle or AAV7m8.SNCG.SIRT1. We conclude that despite minimally affecting the inflammatory response in the optic nerve, AAV7m8-mediated SIRT1 transfer into RGCs has a neuroprotective potential against RGC loss, axon demyelination and vison deficits associated with EAE. Together, these data suggest that SIRT1 exerts direct effects on RGC survival and function. Full article

(This article belongs to the Special Issue Molecular and Cellular Mechanisms of Optic Neuropathies)

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Biomolecules, Volume 12, Issue 6 (June 2022) – 122 articles

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