Biomolecules

14 pages, 1815 KiB

Open AccessEditor’s ChoiceArticle

Changes in Expression in BMP2 and Two Closely Related Genes in Guinea Pig Retinal Pigment Epithelium during Induction and Recovery from Myopia

by So Goto, Yan Zhang, Sonal Aswin Vyas, Qiurong Zhu and Christine F. Wildsoet

Biomolecules 2023, 13(9), 1373; https://doi.org/10.3390/biom13091373 - 11 Sep 2023

Viewed by 1281

Abstract

Purpose: We previously reported differential gene expression of the bone morphogenetic protein 2 (Bmp2) in guinea pig retinal pigment epithelium (RPE) after 1 day of hyperopic defocus, imposed with a negative contact lens (CLs). The study reported here sought to obtain [...] Read more.

Purpose: We previously reported differential gene expression of the bone morphogenetic protein 2 (Bmp2) in guinea pig retinal pigment epithelium (RPE) after 1 day of hyperopic defocus, imposed with a negative contact lens (CLs). The study reported here sought to obtain insights into the temporal profiles of gene expression changes in Bmp2, as well as those of two closely related genes, the inhibitor of DNA binding 3 (Id3) and Noggin (Nog), both during myopia induction and when the CL treatment was terminated to allow recovery from induced myopia. Methods: To induce myopia, 2-week-old pigmented guinea pigs (New Zealand strain, n = 8) wore monocular −10 diopter (D) rigid gas-permeable (RGP) CLs for one week, while the other eye served as a control. Ocular measurements were made at baseline, 3 days, and 7 days after the initiation of CL wear, with treatment then being terminated and additional measurements being made after a further 3 days, 1 week, and 2 weeks. Spherical equivalent refractive errors (SERs), axial length (AL), choroidal thickness (ChT), and scleral thickness (ScT) data were collected using retinoscopy, optical biometry (Lenstar), and spectral domain optical coherence tomography (SD-OCT), respectively. RPE samples were collected from both eyes of the guinea pigs after either 1 day or 1 week of CL wear or 1 day or 2 weeks after its termination, and RNA was subsequently isolated and subjected to quantitative real-time PCR (qRT-PCR) analyses, targeting the Bmp2, Id3, and Nog genes. Results: Mean interocular differences (treated—control) in AL and SER were significantly different from baseline after 3 and 7 days of CL wear, consistent with induced myopia (p < 0.001 for all cases). Termination of CL wear resulted in the normalization (i.e., recovery) of the ALs and SERs of the treated eyes within 7 days, and the earlier significant ChT thinning with CL wear (p = 0004, day 7) was replaced by rapid thickening, which remained significant on day 7 (p = 0.009) but had normalized by day 14. The ChT changes were much smaller in magnitude than the AL changes in both phases. Interocular differences in the ScT showed no significant changes. The Bmp2 and Id3 genes were both significantly downregulated with CL wear, after 1 day (p = 0.012 and 0.016) and 7 days (p = 0.002 and 0.005), while Bmp2 gene expression increased and Nog gene expression decreased after the termination of CL wear, albeit transiently, which was significant on 1 day (p = 0.004 and 0.04) but not 2 weeks later. No change in Id3 gene expression was observed over the latter period. Conclusions: The above patterns of myopia induction and recovery validate this negative RGP-CL model as an alternative to traditional spectacle lens models for guinea pigs. The defocus-driven, sign-dependent changes in the expression of the Bmp2 gene in guinea pig RPE are consistent with observations in chicks and demonstrate the important role of BMP2 in eye growth regulation. Full article

(This article belongs to the Special Issue New Insights into the Molecular Mechanisms of Myopia and Glaucoma)

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17 pages, 2229 KiB

Open AccessEditor’s ChoiceArticle

The Properties and Domain Requirements for Phase Separation of the Sup35 Prion Protein In Vivo

by Bryan Grimes, Walter Jacob, Amanda R. Liberman, Nathan Kim, Xiaohong Zhao, Daniel C. Masison and Lois E. Greene

Biomolecules 2023, 13(9), 1370; https://doi.org/10.3390/biom13091370 - 10 Sep 2023

Cited by 1 | Viewed by 1740

Abstract

The Sup35 prion protein of budding yeast has been reported to undergo phase separation to form liquid droplets both at low pH in vitro and when energy depletion decreases the intracellular pH in vivo. It also has been shown using purified proteins that [...] Read more.

The Sup35 prion protein of budding yeast has been reported to undergo phase separation to form liquid droplets both at low pH in vitro and when energy depletion decreases the intracellular pH in vivo. It also has been shown using purified proteins that this phase separation is driven by the prion domain of Sup35 and does not re-quire its C-terminal domain. In contrast, we now find that a Sup35 fragment consisting of only the N-terminal prion domain and the M-domain does not phase separate in vivo; this phase separation of Sup35 requires the C-terminal domain, which binds Sup45 to form the translation termination complex. The phase-separated Sup35 not only colocalizes with Sup45 but also with Pub1, a stress granule marker protein. In addition, like stress granules, phase separation of Sup35 appears to require mRNA since cycloheximide treatment, which inhibits mRNA release from ribosomes, prevents phase separation of Sup35. Finally, unlike Sup35 in vitro, Sup35 condensates do not disassemble in vivo when the intracellular pH is increased. These results suggest that, in energy-depleted cells, Sup35 forms supramolecular assemblies that differ from the Sup35 liquid droplets that form in vitro. Full article

(This article belongs to the Section Molecular Structure and Dynamics)

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22 pages, 1113 KiB

Open AccessEditor’s ChoiceReview

The Current Status of the Liver Liquid Biopsy in MASH Related HCC: Overview and Future Directions

by Onyinye Ugonabo, Utibe-Abasi Sunday Udoh, Pradeep Kumar Rajan, Heather Reeves, Christina Arcand, Yuto Nakafuku, Tejas Joshi, Rob Finley, Sandrine V. Pierre and Juan Ramon Sanabria

Biomolecules 2023, 13(9), 1369; https://doi.org/10.3390/biom13091369 - 9 Sep 2023

Cited by 2 | Viewed by 2166

Abstract

Metabolic dysfunction-associated steatohepatitis (MASH) is one of the major risk factors for chronic liver disease and hepatocellular carcinoma (HCC). The incidence of MASH in Western countries continues to rise, driving HCC as the third cause of cancer-related death worldwide. HCC has become a [...] Read more.

Metabolic dysfunction-associated steatohepatitis (MASH) is one of the major risk factors for chronic liver disease and hepatocellular carcinoma (HCC). The incidence of MASH in Western countries continues to rise, driving HCC as the third cause of cancer-related death worldwide. HCC has become a major global health challenge, partly from the obesity epidemic promoting metabolic cellular disturbances but also from the paucity of biomarkers for its early detection. Over 50% of HCC cases are clinically present at a late stage, where curative measures are no longer beneficial. Currently, there is a paucity of both specific and sensitive biological markers for the early-stage detection of HCC. The search for biological markers in the diagnosis of early HCC in high-risk populations is intense. We described the potential role of surrogates for a liver biopsy in the screening and monitoring of patients at risk for nesting HCC. Full article

(This article belongs to the Special Issue Cellular Senescence, Aging, and Cancer: Bench to Bedside)

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17 pages, 2907 KiB

Open AccessEditor’s ChoiceArticle

Structure–Activity Relationships of Low Molecular Weight Alginate Oligosaccharide Therapy against Pseudomonas aeruginosa

by Manon F. Pritchard, Lydia C. Powell, Jennifer Y. M. Adams, Georgina Menzies, Saira Khan, Anne Tøndervik, Håvard Sletta, Olav Aarstad, Gudmund Skjåk-Bræk, Stephen McKenna, Niklaas J. Buurma, Damian J. J. Farnell, Philip D. Rye, Katja E. Hill and David W. Thomas

Biomolecules 2023, 13(9), 1366; https://doi.org/10.3390/biom13091366 - 8 Sep 2023

Cited by 1 | Viewed by 1526

Abstract

Low molecular weight alginate oligosaccharides have been shown to exhibit anti-microbial activity against a range of multi-drug resistant bacteria, including Pseudomonas aeruginosa. Previous studies suggested that the disruption of calcium (Ca²⁺)–DNA binding within bacterial biofilms and dysregulation of quorum sensing [...] Read more.

Low molecular weight alginate oligosaccharides have been shown to exhibit anti-microbial activity against a range of multi-drug resistant bacteria, including Pseudomonas aeruginosa. Previous studies suggested that the disruption of calcium (Ca²⁺)–DNA binding within bacterial biofilms and dysregulation of quorum sensing (QS) were key factors in these observed effects. To further investigate the contribution of Ca²⁺ binding, G-block (OligoG) and M-block alginate oligosaccharides (OligoM) with comparable average size DPn 19 but contrasting Ca²⁺ binding properties were prepared. Fourier-transform infrared spectroscopy demonstrated prolonged binding of alginate oligosaccharides to the pseudomonal cell membrane even after hydrodynamic shear treatment. Molecular dynamics simulations and isothermal titration calorimetry revealed that OligoG exhibited stronger interactions with bacterial LPS than OligoM, although this difference was not mirrored by differential reductions in bacterial growth. While confocal laser scanning microscopy showed that both agents demonstrated similar dose-dependent reductions in biofilm formation, OligoG exhibited a stronger QS inhibitory effect and increased potentiation of the antibiotic azithromycin in minimum inhibitory concentration and biofilm assays. This study demonstrates that the anti-microbial effects of alginate oligosaccharides are not purely influenced by Ca²⁺-dependent processes but also by electrostatic interactions that are common to both G-block and M-block structures. Full article

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17 pages, 3685 KiB

Open AccessEditor’s ChoiceArticle

AAV-Mediated Targeting of the Activin A-ACVR1^R206H Signaling in Fibrodysplasia Ossificans Progressiva

by Yeon-Suk Yang, Chujiao Lin, Hong Ma, Jun Xie, Frederick S. Kaplan, Guangping Gao and Jae-Hyuck Shim

Biomolecules 2023, 13(9), 1364; https://doi.org/10.3390/biom13091364 - 8 Sep 2023

Cited by 5 | Viewed by 2079

Abstract

Fibrodysplasia ossificans progressiva (FOP) is an ultra-rare genetic disorder characterized by progressive disabling heterotopic ossification (HO) at extra-skeletal sites. Here, we developed adeno-associated virus (AAV)-based gene therapy that suppresses trauma-induced HO in FOP mice harboring a heterozygous allele of human ACVR1^R206H ( [...] Read more.

Fibrodysplasia ossificans progressiva (FOP) is an ultra-rare genetic disorder characterized by progressive disabling heterotopic ossification (HO) at extra-skeletal sites. Here, we developed adeno-associated virus (AAV)-based gene therapy that suppresses trauma-induced HO in FOP mice harboring a heterozygous allele of human ACVR1^R206H (Acvr1^R206H/+) while limiting the expression in non-skeletal organs such as the brain, heart, lung, liver, and kidney. AAV gene therapy carrying the combination of codon-optimized human ACVR1 (ACVR1^opt) and artificial miRNAs targeting Activin A and its receptor ACVR1^R206H ablated the aberrant activation of BMP-Smad1/5 signaling and the osteogenic differentiation of Acvr1^R206H/+ skeletal progenitors. The local delivery of AAV gene therapy to HO-causing cells in the skeletal muscle resulted in a significant decrease in endochondral bone formation in Acvr1^R206H/+ mice. These mice showed little to no expression in a major AAV-targeted organ, the liver, due to liver-abundant miR-122-mediated repression. Thus, AAV gene therapy is a promising therapeutic strategy to explore in suppressing HO in FOP. Full article

(This article belongs to the Special Issue Fibrodysplasia Ossificans Progressiva (FOP): From Molecular Mechanisms to Therapeutic Strategies)

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20 pages, 2953 KiB

Open AccessEditor’s ChoiceArticle

The Potential Mechanisms behind Loperamide-Induced Cardiac Arrhythmias Associated with Human Abuse and Extreme Overdose

by Hua Rong Lu, Bruce P. Damiano, Mohamed Kreir, Jutta Rohrbacher, Henk van der Linde, Tamerlan Saidov, Ard Teisman and David J. Gallacher

Biomolecules 2023, 13(9), 1355; https://doi.org/10.3390/biom13091355 - 6 Sep 2023

Cited by 1 | Viewed by 2514

Abstract

Loperamide has been a safe and effective treatment for diarrhea for many years. However, many cases of cardiotoxicity with intentional abuse of loperamide ingestion have recently been reported. We evaluated loperamide in in vitro and in vivo cardiac safety models to understand the [...] Read more.

Loperamide has been a safe and effective treatment for diarrhea for many years. However, many cases of cardiotoxicity with intentional abuse of loperamide ingestion have recently been reported. We evaluated loperamide in in vitro and in vivo cardiac safety models to understand the mechanisms for this cardiotoxicity. Loperamide slowed conduction (QRS-duration) starting at 0.3 µM [~1200-fold (×) its human Free Therapeutic Plasma Concentration; FTPC] and reduced the QT-interval and caused cardiac arrhythmias starting at 3 µM (~12,000× FTPC) in an isolated rabbit ventricular-wedge model. Loperamide also slowed conduction and elicited Type II/III A-V block in anesthetized guinea pigs at overdose exposures of 879× and 3802× FTPC. In ion-channel studies, loperamide inhibited hERG (I_Kr)_, I_Na, and I_Ca currents with IC₅₀ values of 0.390 µM, 0.526 µM, and 4.091 µM, respectively (i.e., >1560× FTPC). Additionally, in silico trials in human ventricular action potential models based on these IC50s confirmed that loperamide has large safety margins at therapeutic exposures (≤600× FTPC) and confirmed repolarization abnormalities in the case of extreme doses of loperamide. The studies confirmed the large safety margin for the therapeutic use of loperamide but revealed that at the extreme exposure levels observed in human overdose, loperamide can cause a combination of conduction slowing and alterations in repolarization time, resulting in cardiac proarrhythmia. Loperamide’s inhibition of the I_Na channel and hERG-mediated IKr are the most likely basis for this cardiac electrophysiological toxicity at overdose exposures. The cardiac toxic effects of loperamide at the overdoses could be aggravated by co-medication with other drug(s) causing ion channel inhibition. Full article

(This article belongs to the Special Issue Pharmacology of Cardiovascular Disease)

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12 pages, 924 KiB

Open AccessEditor’s ChoiceReview

Genomics of Wolfram Syndrome 1 (WFS1)

by Sulev Kõks

Biomolecules 2023, 13(9), 1346; https://doi.org/10.3390/biom13091346 - 4 Sep 2023

Cited by 6 | Viewed by 2034

Abstract

Wolfram Syndrome (WFS) is a rare, autosomal, recessive neurogenetic disorder that affects many organ systems. It is characterised by diabetes insipidus, diabetes mellites, optic atrophy, and deafness and, therefore, is also known as DIDMOAD. Nearly 15,000–30,000 people are affected by WFS worldwide, and, [...] Read more.

Wolfram Syndrome (WFS) is a rare, autosomal, recessive neurogenetic disorder that affects many organ systems. It is characterised by diabetes insipidus, diabetes mellites, optic atrophy, and deafness and, therefore, is also known as DIDMOAD. Nearly 15,000–30,000 people are affected by WFS worldwide, and, on average, patients suffering from WFS die at 30 years of age, usually from central respiratory failure caused by massive brain atrophy. The more prevalent of the two kinds of WFS is WFS1, which is a monogenic disease and caused by the loss of the WFS1 gene, whereas WFS2, which is more uncommon, is caused by mutations in the CISD2 gene. Currently, there is no treatment for WFS1 to increase the life expectancy of patients, and the treatments available do not significantly improve their quality of life. Understanding the genetics and the molecular mechanisms of WFS1 is essential to finding a cure. The inability of conventional medications to treat WFS1 points to the need for innovative strategies that must address the fundamental cause: the deletion of the WFS1 gene that leads to the profound ER stress and disturbances in proteostasis. An important approach here is to understand the mechanism of the cell degeneration after the deletion of the WFS1 gene and to describe the differences in these mechanisms for the different tissues. The studies so far have indicated that remarkable clinical heterogeneity is caused by the variable vulnerability caused by WFS1 mutations, and these differences cannot be attributed solely to the positions of mutations in the WFS1 gene. The present review gives a broader overview of the results from genomic studies on the WFS1 mouse model. Full article

(This article belongs to the Special Issue Advance in Genomics of Rare Genetic Diseases)

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57 pages, 33088 KiB

Open AccessEditor’s ChoiceReview

Recent Advances in SARS-CoV-2 Main Protease Inhibitors: From Nirmatrelvir to Future Perspectives

by Andrea Citarella, Alessandro Dimasi, Davide Moi, Daniele Passarella, Angela Scala, Anna Piperno and Nicola Micale

Biomolecules 2023, 13(9), 1339; https://doi.org/10.3390/biom13091339 - 2 Sep 2023

Cited by 16 | Viewed by 2686

Abstract

The main protease (M^pro) plays a pivotal role in the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is considered a highly conserved viral target. Disruption of the catalytic activity of M^pro produces a detrimental effect on the [...] Read more.

The main protease (M^pro) plays a pivotal role in the replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is considered a highly conserved viral target. Disruption of the catalytic activity of M^pro produces a detrimental effect on the course of the infection, making this target one of the most attractive for the treatment of COVID-19. The current success of the SARS-CoV-2 M^pro inhibitor Nirmatrelvir, the first oral drug for the treatment of severe forms of COVID-19, has further focused the attention of researchers on this important viral target, making the search for new M^pro inhibitors a thriving and exciting field for the development of antiviral drugs active against SARS-CoV-2 and related coronaviruses. Full article

(This article belongs to the Special Issue State of the Art in Antiviral Therapy and Viral Diseases Diagnosis: An Update to 2022-2023)

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22 pages, 26292 KiB

Open AccessEditor’s ChoiceArticle

ABCD1 Transporter Deficiency Results in Altered Cholesterol Homeostasis

by Agnieszka Buda, Sonja Forss-Petter, Rong Hua, Yorrick Jaspers, Mark Lassnig, Petra Waidhofer-Söllner, Stephan Kemp, Peter Kim, Isabelle Weinhofer and Johannes Berger

Biomolecules 2023, 13(9), 1333; https://doi.org/10.3390/biom13091333 - 31 Aug 2023

Cited by 3 | Viewed by 2098

Abstract

X-linked adrenoleukodystrophy (X-ALD), the most common peroxisomal disorder, is caused by mutations in the peroxisomal transporter ABCD1, resulting in the accumulation of very long-chain fatty acids (VLCFA). Strongly affected cell types, such as oligodendrocytes, adrenocortical cells and macrophages, exhibit high cholesterol turnover. Here, [...] Read more.

X-linked adrenoleukodystrophy (X-ALD), the most common peroxisomal disorder, is caused by mutations in the peroxisomal transporter ABCD1, resulting in the accumulation of very long-chain fatty acids (VLCFA). Strongly affected cell types, such as oligodendrocytes, adrenocortical cells and macrophages, exhibit high cholesterol turnover. Here, we investigated how ABCD1 deficiency affects cholesterol metabolism in human X-ALD patient-derived fibroblasts and CNS tissues of Abcd1-deficient mice. Lipidome analyses revealed increased levels of cholesterol esters (CE), containing both saturated VLCFA and mono/polyunsaturated (V)LCFA. The elevated CE(26:0) and CE(26:1) levels remained unchanged in LXR agonist-treated Abcd1 KO mice despite reduced total C26:0. Under high-cholesterol loading, gene expression of SOAT1, converting cholesterol to CE and lipid droplet formation were increased in human X-ALD fibroblasts versus healthy control fibroblasts. However, the expression of NCEH1, catalysing CE hydrolysis and the cholesterol transporter ABCA1 and cholesterol efflux were also upregulated. Elevated Soat1 and Abca1 expression and lipid droplet content were confirmed in the spinal cord of X-ALD mice, where expression of the CNS cholesterol transporter Apoe was also elevated. The extent of peroxisome-lipid droplet co-localisation appeared low and was not impaired by ABCD1-deficiency in cholesterol-loaded primary fibroblasts. Finally, addressing steroidogenesis, progesterone-induced cortisol release was amplified in X-ALD fibroblasts. These results link VLCFA to cholesterol homeostasis and justify further consideration of therapeutic approaches towards reducing VLCFA and cholesterol levels in X-ALD. Full article

(This article belongs to the Special Issue The Role of Peroxisome in Cell Functions and Pathological Consequences of Its Dysfunction)

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21 pages, 3006 KiB

Open AccessEditor’s ChoiceArticle

Neuroactive Steroid–Gut Microbiota Interaction in T2DM Diabetic Encephalopathy

by Silvia Diviccaro, Lucia Cioffi, Rocco Piazza, Donatella Caruso, Roberto Cosimo Melcangi and Silvia Giatti

Biomolecules 2023, 13(9), 1325; https://doi.org/10.3390/biom13091325 - 29 Aug 2023

Viewed by 1344

Abstract

The pathological consequences of type 2 diabetes mellitus (T2DM) also involve the central nervous system; indeed, T2DM patients suffer from learning and memory disabilities with a higher risk of developing dementia. Although several factors have been proposed as possible contributors, how neuroactive steroids [...] Read more.

The pathological consequences of type 2 diabetes mellitus (T2DM) also involve the central nervous system; indeed, T2DM patients suffer from learning and memory disabilities with a higher risk of developing dementia. Although several factors have been proposed as possible contributors, how neuroactive steroids and the gut microbiome impact brain pathophysiology in T2DM remain unexplored. On this basis, in male Zucker diabetic fatty (ZDF) rats, we studied whether T2DM alters memory abilities using the novel object recognition test, neuroactive steroid levels by liquid chromatography–tandem mass spectrometry, hippocampal parameters using molecular assessments, and gut microbiome composition using 16S next-generation sequencing. Results obtained reveal that T2DM worsens memory abilities and that these are correlated with increased levels of corticosterone in plasma and with a decrease in allopregnanolone in the hippocampus, where neuroinflammation, oxidative stress, and mitochondrial dysfunction were reported. Interestingly, our analysis highlighted a small group of taxa strictly related to both memory impairment and neuroactive steroid levels. Overall, the data underline an interesting role for allopregnanolone and microbiota that may represent candidates for the development of therapeutic strategies. Full article

(This article belongs to the Special Issue Role of Neuroactive Steroids in Health and Disease)

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14 pages, 813 KiB

Open AccessEditor’s ChoiceReview

Advances in Dystrophinopathy Diagnosis and Therapy

by Fawzy A. Saad, Gabriele Siciliano and Corrado Angelini

Biomolecules 2023, 13(9), 1319; https://doi.org/10.3390/biom13091319 - 28 Aug 2023

Cited by 7 | Viewed by 3575

Abstract

Dystrophinopathies are x-linked muscular disorders which emerge from mutations in the Dystrophin gene, including Duchenne and Becker muscular dystrophy, and dilated cardiomyopathy. However, Duchenne muscular dystrophy interconnects with bone loss and osteoporosis, which are exacerbated by glucocorticoids therapy. Procedures for diagnosing dystrophinopathies include [...] Read more.

Dystrophinopathies are x-linked muscular disorders which emerge from mutations in the Dystrophin gene, including Duchenne and Becker muscular dystrophy, and dilated cardiomyopathy. However, Duchenne muscular dystrophy interconnects with bone loss and osteoporosis, which are exacerbated by glucocorticoids therapy. Procedures for diagnosing dystrophinopathies include creatine kinase assay, haplotype analysis, Southern blot analysis, immunological analysis, multiplex PCR, multiplex ligation-dependent probe amplification, Sanger DNA sequencing, and next generation DNA sequencing. Pharmacological therapy for dystrophinopathies comprises glucocorticoids (prednisone, prednisolone, and deflazacort), vamorolone, and ataluren. However, angiotensin-converting enzyme (ACE) inhibitors, angiotensin receptor blockers (ARBs), and β-blockers are the first-line to prevent dilated cardiomyopathy in dystrophinopathy patients. Duchenne muscular dystrophy gene therapy strategies involve gene transfer, exon skipping, exon reframing, and CRISPR gene editing. Eteplirsen, an antisense-oligonucleotide drug for skipping exon 51 from the Dystrophin gene, is available on the market, which may help up to 14% of Duchenne muscular dystrophy patients. There are various FDA-approved exon skipping drugs including ExonDys-51 for exon 51, VyonDys-53 and Viltolarsen for exon 53 and AmonDys-45 for exon 45 skipping. Other antisense oligonucleotide drugs in the pipeline include casimersen for exon 45, suvodirsen for exon 51, and golodirsen for exon 53 skipping. Advances in the diagnosis and therapy of dystrophinopathies offer new perspectives for their early discovery and care. Full article

(This article belongs to the Special Issue Molecular Basis and Translational Research in Metabolic Myopathies: A Themed Issue in Honor of Professor Corrado Angelini)

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15 pages, 2820 KiB

Open AccessEditor’s ChoiceArticle

Chronic Aripiprazole and Trazodone Polypharmacy Effects on Systemic and Brain Cholesterol Biosynthesis

by Zeljka Korade, Allison Anderson, Marta Balog, Keri A. Tallman, Ned A. Porter and Karoly Mirnics

Biomolecules 2023, 13(9), 1321; https://doi.org/10.3390/biom13091321 - 28 Aug 2023

Cited by 1 | Viewed by 2682

Abstract

The concurrent use of several medications is a common practice in the treatment of complex psychiatric conditions. One such commonly used combination is aripiprazole (ARI), an antipsychotic, and trazodone (TRZ), an antidepressant. In addition to their effects on dopamine and serotonin systems, both [...] Read more.

The concurrent use of several medications is a common practice in the treatment of complex psychiatric conditions. One such commonly used combination is aripiprazole (ARI), an antipsychotic, and trazodone (TRZ), an antidepressant. In addition to their effects on dopamine and serotonin systems, both of these compounds are inhibitors of the 7-dehydrocholesterol reductase (DHCR7) enzyme. To evaluate the systemic and nervous system distribution of ARI and TRZ and their effects on cholesterol biosynthesis, adult mice were treated with both ARI and TRZ for 21 days. The parent drugs, their metabolites, and sterols were analyzed in the brain and various organs of mice using LC-MS/MS. The analyses revealed that ARI, TRZ, and their metabolites were readily detectable in the brain and organs, leading to changes in the sterol profile. The levels of medications, their metabolites, and sterols differed across tissues with notable sex differences. Female mice showed higher turnover of ARI and more cholesterol clearance in the brain, with several post-lanosterol intermediates significantly altered. In addition to interfering with sterol biosynthesis, ARI and TRZ exposure led to decreased ionized calcium-binding adaptor molecule 1 (IBA1) and increased DHCR7 protein expression in the cortex. Changes in sterol profile have been also identified in the spleen, liver, and serum, underscoring the systemic effect of ARI and TRZ on sterol biosynthesis. Long-term use of concurrent ARI and TRZ warrants further studies to fully evaluate the lasting consequences of altered sterol biosynthesis on the whole body. Full article

(This article belongs to the Special Issue Brain Sterols: Biosynthesis and Physiology in Health and Disease)

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18 pages, 4099 KiB

Open AccessEditor’s ChoiceArticle

Pegylated Liposomal Alendronate Biodistribution, Immune Modulation, and Tumor Growth Inhibition in a Murine Melanoma Model

by Md. Rakibul Islam, Jalpa Patel, Patricia Ines Back, Hilary Shmeeda, Raja Reddy Kallem, Claire Shudde, Maciej Markiewski, William C. Putnam, Alberto A. Gabizon and Ninh M. La-Beck

Biomolecules 2023, 13(9), 1309; https://doi.org/10.3390/biom13091309 - 26 Aug 2023

Cited by 2 | Viewed by 1915

Abstract

While tumor-associated macrophages (TAM) have pro-tumoral activity, the ablation of macrophages in cancer may be undesirable since they also have anti-tumoral functions, including T cell priming and activation against tumor antigens. Alendronate is a potent amino-bisphosphonate that modulates the function of macrophages in [...] Read more.

While tumor-associated macrophages (TAM) have pro-tumoral activity, the ablation of macrophages in cancer may be undesirable since they also have anti-tumoral functions, including T cell priming and activation against tumor antigens. Alendronate is a potent amino-bisphosphonate that modulates the function of macrophages in vitro, with potential as an immunotherapy if its low systemic bioavailability can be addressed. We repurposed alendronate in a non-leaky and long-circulating liposomal carrier similar to that of the clinically approved pegylated liposomal doxorubicin to facilitate rapid clinical translation. Here, we tested liposomal alendronate (PLA) as an immunotherapeutic agent for cancer in comparison with a standard of care immunotherapy, a PD-1 immune checkpoint inhibitor. We showed that the PLA induced bone marrow-derived murine non-activated macrophages and M2-macrophages to polarize towards an M1-functionality, as evidenced by gene expression, cytokine secretion, and lipidomic profiles. Free alendronate had negligible effects, indicating that liposome encapsulation is necessary for the modulation of macrophage activity. In vivo, the PLA showed significant accumulation in tumor and tumor-draining lymph nodes, sites of tumor immunosuppression that are targets of immunotherapy. The PLA remodeled the tumor microenvironment towards a less immunosuppressive milieu, as indicated by a decrease in TAM and helper T cells, and inhibited the growth of established tumors in the B16-OVA melanoma model. The improved bioavailability and the beneficial effects of PLA on macrophages suggest its potential application as immunotherapy that could synergize with T-cell-targeted therapies and chemotherapies to induce immunogenic cell death. PLA warrants further clinical development, and these clinical trials should incorporate tumor and blood biomarkers or immunophenotyping studies to verify the anti-immunosuppressive effect of PLA in humans. Full article

(This article belongs to the Special Issue Liposomes for Drug Delivery: Recent Advances and Discoveries)

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33 pages, 5052 KiB

Open AccessFeature PaperEditor’s ChoiceReview

Lipid Peroxidation and Antioxidant Protection

by Luca Valgimigli

Biomolecules 2023, 13(9), 1291; https://doi.org/10.3390/biom13091291 - 24 Aug 2023

Cited by 15 | Viewed by 3768

Abstract

Lipid peroxidation (LP) is the most important type of oxidative-radical damage in biological systems, owing to its interplay with ferroptosis and to its role in secondary damage to other biomolecules, such as proteins. The chemistry of LP and its biological consequences are reviewed [...] Read more.

Lipid peroxidation (LP) is the most important type of oxidative-radical damage in biological systems, owing to its interplay with ferroptosis and to its role in secondary damage to other biomolecules, such as proteins. The chemistry of LP and its biological consequences are reviewed with focus on the kinetics of the various processes, which helps understand the mechanisms and efficacy of antioxidant strategies. The main types of antioxidants are discussed in terms of structure–activity rationalization, with focus on mechanism and kinetics, as well as on their potential role in modulating ferroptosis. Phenols, pyri(mi)dinols, antioxidants based on heavy chalcogens (Se and Te), diarylamines, ascorbate and others are addressed, along with the latest unconventional antioxidant strategies based on the double-sided role of the superoxide/hydroperoxyl radical system. Full article

(This article belongs to the Special Issue Biomarkers of Oxidative and Radical Stress)

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17 pages, 2326 KiB

Open AccessEditor’s ChoiceArticle

Peroxisomal NAD(H) Homeostasis in the Yeast Debaryomyces hansenii Depends on Two Redox Shuttles and the NAD⁺ Carrier, Pmp47

by Selva Turkolmez, Serhii Chornyi, Sondos Alhajouj, Lodewijk IJlst, Hans R. Waterham, Phil J. Mitchell, Ewald H. Hettema and Carlo W. T. van Roermund

Biomolecules 2023, 13(9), 1294; https://doi.org/10.3390/biom13091294 - 24 Aug 2023

Cited by 4 | Viewed by 1654

Abstract

Debaryomyces hansenii is considered an unconventional yeast with a strong biotechnological potential, which can produce and store high amounts of lipids. However, relatively little is known about its lipid metabolism, and genetic tools for this yeast have been limited. The aim of this [...] Read more.

Debaryomyces hansenii is considered an unconventional yeast with a strong biotechnological potential, which can produce and store high amounts of lipids. However, relatively little is known about its lipid metabolism, and genetic tools for this yeast have been limited. The aim of this study was to explore the fatty acid β-oxidation pathway in D. hansenii. To this end, we employed recently developed methods to generate multiple gene deletions and tag open reading frames with GFP in their chromosomal context in this yeast. We found that, similar as in other yeasts, the β-oxidation of fatty acids in D. hansenii was restricted to peroxisomes. We report a series of experiments in D. hansenii and the well-studied yeast Saccharomyces cerevisiae that show that the homeostasis of NAD⁺ in D. hansenii peroxisomes is dependent upon the peroxisomal membrane protein Pmp47 and two peroxisomal dehydrogenases, Mdh3 and Gpd1, which both export reducing equivalents produced during β-oxidation to the cytosol. Pmp47 is the first identified NAD⁺ carrier in yeast peroxisomes. Full article

(This article belongs to the Special Issue The Role of Peroxisome in Cell Functions and Pathological Consequences of Its Dysfunction)

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17 pages, 2151 KiB

Open AccessFeature PaperEditor’s ChoiceReview

A Novel Gliotransmitter, L-β-Aminoisobutyric Acid, Contributes to Pathophysiology of Clinical Efficacies and Adverse Reactions of Clozapine

by Kouji Fukuyama, Eishi Motomura and Motohiro Okada

Biomolecules 2023, 13(9), 1288; https://doi.org/10.3390/biom13091288 - 23 Aug 2023

Cited by 3 | Viewed by 1463

Abstract

Clozapine is listed as one of the most effective antipsychotics and has been approved for treating treatment-resistant schizophrenia (TRS); however, several type A and B adverse reactions, including weight gain, metabolic complications, cardiotoxicity, convulsions, and discontinuation syndromes, exist. The critical mechanisms of clinical [...] Read more.

Clozapine is listed as one of the most effective antipsychotics and has been approved for treating treatment-resistant schizophrenia (TRS); however, several type A and B adverse reactions, including weight gain, metabolic complications, cardiotoxicity, convulsions, and discontinuation syndromes, exist. The critical mechanisms of clinical efficacy for schizophrenia, TRS, and adverse reactions of clozapine have not been elucidated. Recently, the GABA isomer L-β-aminoisobutyric acid (L-BAIBA), a protective myokine in the peripheral organs, was identified as a candidate novel transmission modulator in the central nervous system (CNS). L-BAIBA activates adenosine monophosphate-activated protein kinase (AMPK) signalling in both the peripheral organs and CNS. Activated AMPK signalling in peripheral organs is an established major target for treating insulin-resistant diabetes, whereas activated AMPK signalling in the hypothalamus contributes to the pathophysiology of weight gain and metabolic disturbances. Clozapine increases L-BAIBA synthesis in the hypothalamus. In addition, the various functions of L-BAIBA in the CNS have recently been elucidated, including as an activator of GABA-B and group-III metabotropic glutamate (III-mGlu) receptors. Considering the expressions of GABA-B and III-mGlu receptors (localised in the presynaptic regions), the activation of GABA-B and III-mGlu receptors can explain the distinct therapeutic advantages of clozapine in schizophrenia or TRS associated with N-methyl-D-aspartate (NMDA) receptor disturbance compared with other atypical antipsychotics via the inhibition of the persistent tonic hyperactivation of thalamocortical glutamatergic transmission in the prefrontal cortex. L-BAIBA has also been identified as a gliotransmitter, and a detailed exploration of the function of L-BAIBA in tripartite synaptic transmission can further elucidate the pathophysiology of effectiveness for treating TRS and/or specific adverse reactions of clozapine. Full article

(This article belongs to the Special Issue NMDA Receptor in Health and Diseases: 2nd Edition)

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26 pages, 848 KiB

Open AccessEditor’s ChoiceReview

A Comprehensive Update on Late-Onset Pompe Disease

by Beatrice Labella, Stefano Cotti Piccinelli, Barbara Risi, Filomena Caria, Simona Damioli, Enrica Bertella, Loris Poli, Alessandro Padovani and Massimiliano Filosto

Biomolecules 2023, 13(9), 1279; https://doi.org/10.3390/biom13091279 - 22 Aug 2023

Cited by 1 | Viewed by 3825

Abstract

Pompe disease (PD) is an autosomal recessive disorder caused by mutations in the GAA gene that lead to a deficiency in the acid alpha-glucosidase enzyme. Two clinical presentations are usually considered, named infantile-onset Pompe disease (IOPD) and late-onset Pompe disease (LOPD), which differ [...] Read more.

Pompe disease (PD) is an autosomal recessive disorder caused by mutations in the GAA gene that lead to a deficiency in the acid alpha-glucosidase enzyme. Two clinical presentations are usually considered, named infantile-onset Pompe disease (IOPD) and late-onset Pompe disease (LOPD), which differ in age of onset, organ involvement, and severity of disease. Assessment of acid alpha-glucosidase activity on a dried blood spot is the first-line screening test, which needs to be confirmed by genetic analysis in case of suspected deficiency. LOPD is a multi-system disease, thus requiring a multidisciplinary approach for efficacious management. Enzyme replacement therapy (ERT), which was introduced over 15 years ago, changes the natural progression of the disease. However, it has limitations, including a reduction in efficacy over time and heterogeneous therapeutic responses among patients. Novel therapeutic approaches, such as gene therapy, are currently under study. We provide a comprehensive review of diagnostic advances in LOPD and a critical discussion about the advantages and limitations of current and future treatments. Full article

(This article belongs to the Special Issue Molecular Basis and Translational Research in Metabolic Myopathies: A Themed Issue in Honor of Professor Corrado Angelini)

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14 pages, 849 KiB

Open AccessEditor’s ChoiceReview

The Ca²⁺ Sensor STIM in Human Diseases

by Alejandro Berna-Erro, Jose Sanchez-Collado, Joel Nieto-Felipe, Alvaro Macias-Diaz, Pedro C. Redondo, Tarik Smani, Jose J. Lopez, Isaac Jardin and Juan A. Rosado

Biomolecules 2023, 13(9), 1284; https://doi.org/10.3390/biom13091284 - 22 Aug 2023

Viewed by 1659

Abstract

The STIM family of proteins plays a crucial role in a plethora of cellular functions through the regulation of store-operated Ca²⁺ entry (SOCE) and, thus, intracellular calcium homeostasis. The two members of the mammalian STIM family, STIM1 and STIM2, are transmembrane proteins [...] Read more.

The STIM family of proteins plays a crucial role in a plethora of cellular functions through the regulation of store-operated Ca²⁺ entry (SOCE) and, thus, intracellular calcium homeostasis. The two members of the mammalian STIM family, STIM1 and STIM2, are transmembrane proteins that act as Ca²⁺ sensors in the endoplasmic reticulum (ER) and, upon Ca²⁺ store discharge, interact with and activate the Orai/CRACs in the plasma membrane. Dysregulation of Ca²⁺ signaling leads to the pathogenesis of a variety of human diseases, including neurodegenerative disorders, cardiovascular diseases, cancer, and immune disorders. Therefore, understanding the mechanisms underlying Ca²⁺ signaling pathways is crucial for developing therapeutic strategies targeting these diseases. This review focuses on several rare conditions associated with STIM1 mutations that lead to either gain- or loss-of-function, characterized by myopathy, hematological and immunological disorders, among others, and due to abnormal activation of CRACs. In addition, we summarize the current evidence concerning STIM2 allele duplication and deletion associated with language, intellectual, and developmental delay, recurrent pulmonary infections, microcephaly, facial dimorphism, limb anomalies, hypogonadism, and congenital heart defects. Full article

(This article belongs to the Special Issue Dysregulation of Calcium Signaling in Pathological Processes)

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16 pages, 4982 KiB

Open AccessEditor’s ChoiceArticle

Hybrid Material Based on Vaccinium myrtillus L. Extract and Gold Nanoparticles Reduces Oxidative Stress and Inflammation in Hepatic Stellate Cells Exposed to TGF-β

by Mara Filip, Ioana Baldea, Luminita David, Bianca Moldovan, Gabriel Cristian Flontas, Sergiu Macavei, Dana Maria Muntean, Nicoleta Decea, Adrian Bogdan Tigu and Simona Valeria Clichici

Biomolecules 2023, 13(8), 1271; https://doi.org/10.3390/biom13081271 - 20 Aug 2023

Cited by 2 | Viewed by 1248

Abstract

(1) Background: The study aimed to investigate the impact of gold nanoparticles capped with Cornus sanguinea (NPCS) and mixed with a fruit extract (Vaccinum myrtillus L.—VL) on human hepatic stellate cells (LX-2) exposed to TGF-β. (2) Methods: NPCS were characterized by UV-Vis, [...] Read more.

(1) Background: The study aimed to investigate the impact of gold nanoparticles capped with Cornus sanguinea (NPCS) and mixed with a fruit extract (Vaccinum myrtillus L.—VL) on human hepatic stellate cells (LX-2) exposed to TGF-β. (2) Methods: NPCS were characterized by UV-Vis, transmission electron microscopy (TEM), zeta potential measurement, X-ray diffraction (XRD) and energy dispersive spectroscopy (EDX). The cytotoxic effects of VL, NPCS and of the hybrid compounds obtained by mixing the two components in variable proportions (NPCS-VL) were assessed. LDH activity, MDA levels, secretion of inflammation markers, the expression of fibrogenesis markers and collagen I synthesis were estimated after treating the cells with a mixture of 25:25 μg/mL NPCS and VL. (3) Results: TEM analysis showed that NPCS had spherical morphology and homogenous distribution, while their formation and elemental composition were confirmed by XRD and EDX analysis. TGF-β increased cell membrane damage as well as secretion of IL-1β, IL-1α and TLR4. It also amplified the expression of α-SMA and type III collagen and induced collagen I deposition. NPCS administration reduced the inflammation caused by TGF-β and downregulated α-SMA expression. VL diminished LDH activity and the secretion of proinflammatory cytokines. The NPCS-VL mixture maintained IL-1β, IL-1α, TLR4 and LDH at low levels after TGF-β exposure, but it enhanced collagen III expression. (4) Conclusions: The mixture of NPCS and VL improved cell membrane damage and inflammation triggered by TGF-β and mitigated collagen I deposition, but it increased the expression of collagen III, suggestive of a fibrogenetic effect of the hybrid material. Full article

(This article belongs to the Special Issue Bionanomaterials: Synthesis, Characterization, Toxicity and Biomedical Applications (Volume II))

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34 pages, 560 KiB

Open AccessEditor’s ChoiceReview

Alpha-Synuclein in Peripheral Tissues as a Possible Marker for Neurological Diseases and Other Medical Conditions

by Félix Javier Jiménez-Jiménez, Hortensia Alonso-Navarro, Elena García-Martín, Diego Santos-García, Iván Martínez-Valbuena and José A. G. Agúndez

Biomolecules 2023, 13(8), 1263; https://doi.org/10.3390/biom13081263 - 18 Aug 2023

Cited by 6 | Viewed by 1822

Abstract

The possible usefulness of alpha-synuclein (aSyn) determinations in peripheral tissues (blood cells, salivary gland biopsies, olfactory mucosa, digestive tract, skin) and in biological fluids, except for cerebrospinal fluid (serum, plasma, saliva, feces, urine), as a marker of several diseases, has been the subject [...] Read more.

The possible usefulness of alpha-synuclein (aSyn) determinations in peripheral tissues (blood cells, salivary gland biopsies, olfactory mucosa, digestive tract, skin) and in biological fluids, except for cerebrospinal fluid (serum, plasma, saliva, feces, urine), as a marker of several diseases, has been the subject of numerous publications. This narrative review summarizes data from studies trying to determine the role of total, oligomeric, and phosphorylated aSyn determinations as a marker of various diseases, especially PD and other alpha-synucleinopathies. In summary, the results of studies addressing the determinations of aSyn in its different forms in peripheral tissues (especially in platelets, skin, and digestive tract, but also salivary glands and olfactory mucosa), in combination with other potential biomarkers, could be a useful tool to discriminate PD from controls and from other causes of parkinsonisms, including synucleinopathies. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Alpha-Synuclein in Parkinson's Disease and Other Synucleinopathies)

29 pages, 2676 KiB

Open AccessEditor’s ChoiceReview

Cyclophilin D in Mitochondrial Dysfunction: A Key Player in Neurodegeneration?

by Gabriele Coluccino, Valentina Pia Muraca, Alessandra Corazza and Giovanna Lippe

Biomolecules 2023, 13(8), 1265; https://doi.org/10.3390/biom13081265 - 18 Aug 2023

Viewed by 1952

Abstract

Mitochondrial dysfunction plays a pivotal role in numerous complex diseases. Understanding the molecular mechanisms by which the “powerhouse of the cell” turns into the “factory of death” is an exciting yet challenging task that can unveil new therapeutic targets. The mitochondrial matrix protein [...] Read more.

Mitochondrial dysfunction plays a pivotal role in numerous complex diseases. Understanding the molecular mechanisms by which the “powerhouse of the cell” turns into the “factory of death” is an exciting yet challenging task that can unveil new therapeutic targets. The mitochondrial matrix protein CyPD is a peptidylprolyl cis-trans isomerase involved in the regulation of the permeability transition pore (mPTP). The mPTP is a multi-conductance channel in the inner mitochondrial membrane whose dysregulated opening can ultimately lead to cell death and whose involvement in pathology has been extensively documented over the past few decades. Moreover, several mPTP-independent CyPD interactions have been identified, indicating that CyPD could be involved in the fine regulation of several biochemical pathways. To further enrich the picture, CyPD undergoes several post-translational modifications that regulate both its activity and interaction with its clients. Here, we will dissect what is currently known about CyPD and critically review the most recent literature about its involvement in neurodegenerative disorders, focusing on Alzheimer’s Disease and Parkinson’s Disease, supporting the notion that CyPD could serve as a promising therapeutic target for the treatment of such conditions. Notably, significant efforts have been made to develop CyPD-specific inhibitors, which hold promise for the treatment of such complex disorders. Full article

(This article belongs to the Special Issue Mitochondria and Central Nervous System Disorders II)

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32 pages, 16488 KiB

Open AccessEditor’s ChoiceArticle

Local Control Model of a Human Ventricular Myocyte: An Exploration of Frequency-Dependent Changes and Calcium Sparks

by Jerome Anthony E. Alvarez, M. Saleet Jafri and Aman Ullah

Biomolecules 2023, 13(8), 1259; https://doi.org/10.3390/biom13081259 - 17 Aug 2023

Viewed by 2279

Abstract

Calcium (Ca²⁺) sparks are the elementary events of excitation–contraction coupling, yet they are not explicitly represented in human ventricular myocyte models. A stochastic ventricular cardiomyocyte human model that adapts to intracellular Ca²⁺ ([Ca²⁺]_i) dynamics, spark regulation, [...] Read more.

Calcium (Ca²⁺) sparks are the elementary events of excitation–contraction coupling, yet they are not explicitly represented in human ventricular myocyte models. A stochastic ventricular cardiomyocyte human model that adapts to intracellular Ca²⁺ ([Ca²⁺]_i) dynamics, spark regulation, and frequency-dependent changes in the form of locally controlled Ca²⁺ release was developed. The 20,000 CRUs in this model are composed of 9 individual LCCs and 49 RyRs that function as couplons. The simulated action potential duration at 1 Hz steady-state pacing is ~0.280 s similar to human ventricular cell recordings. Rate-dependence experiments reveal that APD shortening mechanisms are largely contributed by the L-type calcium channel inactivation, RyR open fraction, and [Ca²⁺]_myo concentrations. The dynamic slow-rapid-slow pacing protocol shows that RyR open probability during high pacing frequency (2.5 Hz) switches to an adapted “nonconducting” form of Ca²⁺-dependent transition state. The predicted force was also observed to be increased in high pacing, but the SR Ca²⁺ fractional release was lower due to the smaller difference between diastolic and systolic [Ca²⁺]_SR. Restitution analysis through the S1S2 protocol and increased LCC Ca²⁺-dependent activation rate show that the duration of LCC opening helps modulate its effects on the APD restitution at different diastolic intervals. Ultimately, a longer duration of calcium sparks was observed in relation to the SR Ca²⁺ loading at high pacing rates. Overall, this study demonstrates the spontaneous Ca²⁺ release events and ion channel responses throughout various stimuli. Full article

(This article belongs to the Special Issue Computational Insights into Calcium Signaling)

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16 pages, 1101 KiB

Open AccessEditor’s ChoiceReview

Endometriosis-Associated Ovarian Carcinomas: How PI3K/AKT/mTOR Pathway Affects Their Pathogenesis

by Tatiana S. Driva, Christoph Schatz and Johannes Haybaeck

Biomolecules 2023, 13(8), 1253; https://doi.org/10.3390/biom13081253 - 16 Aug 2023

Cited by 11 | Viewed by 2537

Abstract

Ovarian clear cell (OCCC) and endometrioid (EnOC) carcinomas are often subsumed under the umbrella term “endometriosis-associated ovarian cancer” (EAOC), since they frequently arise from ectopic endometrium settled in the ovaries. The phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway is [...] Read more.

Ovarian clear cell (OCCC) and endometrioid (EnOC) carcinomas are often subsumed under the umbrella term “endometriosis-associated ovarian cancer” (EAOC), since they frequently arise from ectopic endometrium settled in the ovaries. The phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway is known to be aberrantly activated both in endometriosis and EAOC; however, its role in the progression of endometriosis to ovarian cancer remains unclear. In fact, cancer-associated alterations in the mTOR pathway may be found in normal uterine epithelium, likely acting as a first step towards ovarian cancer, through the intermediary stage of endometriosis. This review aims to summarize the current knowledge regarding mTOR signaling dysregulation in the uterine endometrium, endometriosis, and EAOC while focusing on the interconnections between the PI3K/AKT/mTOR pathway and other signaling molecules that give rise to synergistic molecular mechanisms triggering ovarian cancer development in the presence of endometriosis. Full article

(This article belongs to the Special Issue Molecular and Cell Biology in Endometriosis and Endometrial Cancer)

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19 pages, 6423 KiB

Open AccessEditor’s ChoiceArticle

Circulating H3K27 Methylated Nucleosome Plasma Concentration: Synergistic Information with Circulating Tumor DNA Molecular Profiling

by Emmanuel Grolleau, Julie Candiracci, Gaelle Lescuyer, David Barthelemy, Nazim Benzerdjeb, Christine Haon, Florence Geiguer, Margaux Raffin, Nathalie Hardat, Julie Balandier, Rémi Rabeuf, Lara Chalabreysse, Anne-Sophie Wozny, Guillaume Rommelaere, Claire Rodriguez-Lafrasse, Fabien Subtil, Sébastien Couraud, Marielle Herzog and Lea Payen-Gay

Biomolecules 2023, 13(8), 1255; https://doi.org/10.3390/biom13081255 - 16 Aug 2023

Cited by 2 | Viewed by 1775

Abstract

The molecular profiling of circulating tumor DNA (ctDNA) is a helpful tool not only in cancer treatment, but also in the early detection of relapse. However, the clinical interpretation of a ctDNA negative result remains challenging. The characterization of circulating nucleosomes (carrying cell-free [...] Read more.

The molecular profiling of circulating tumor DNA (ctDNA) is a helpful tool not only in cancer treatment, but also in the early detection of relapse. However, the clinical interpretation of a ctDNA negative result remains challenging. The characterization of circulating nucleosomes (carrying cell-free DNA) and associated epigenetic modifications (playing a key role in the tumorigenesis of different cancers) may provide useful information for patient management, by supporting the contributive value of ctDNA molecular profiling. Significantly elevated concentrations of H3K27Me3 nucleosomes were found in plasmas at the diagnosis, and during the follow-up, of NSCLC patients, compared to healthy donors (p-value < 0.0001). By combining the H3K27Me3 level and the ctDNA molecular profile, we found that 25.5% of the patients had H3K27Me3 levels above the cut off, and no somatic alteration was detected at diagnosis. This strongly supports the presence of non-mutated ctDNA in the corresponding plasma. During the patient follow-up, a high H3K27Me3-nucleosome level was found in 15.1% of the sample, despite no somatic mutations being detected, allowing the identification of disease progression from 43.1% to 58.2% over molecular profiling alone. Measuring H3K27Me3-nucleosome levels in combination with ctDNA molecular profiling may improve confidence in the negative molecular result for cfDNA in lung cancer at diagnosis, and may also be a promising biomarker for molecular residual disease (MRD) monitoring, during and/or after treatment. Full article

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

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19 pages, 1779 KiB

Open AccessEditor’s ChoiceReview

The Molecular and Genetic Mechanisms of Inherited Bone Marrow Failure Syndromes: The Role of Inflammatory Cytokines in Their Pathogenesis

by Nozomu Kawashima, Valentino Bezzerri and Seth J. Corey

Biomolecules 2023, 13(8), 1249; https://doi.org/10.3390/biom13081249 - 16 Aug 2023

Cited by 2 | Viewed by 3119

Abstract

Inherited bone marrow failure syndromes (IBMFSs) include Fanconi anemia, Diamond–Blackfan anemia, Shwachman–Diamond syndrome, dyskeratosis congenita, severe congenital neutropenia, and other rare entities such as GATA2 deficiency and SAMD9/9L mutations. The IBMFS monogenic disorders were first recognized by their phenotype. Exome sequencing has validated [...] Read more.

Inherited bone marrow failure syndromes (IBMFSs) include Fanconi anemia, Diamond–Blackfan anemia, Shwachman–Diamond syndrome, dyskeratosis congenita, severe congenital neutropenia, and other rare entities such as GATA2 deficiency and SAMD9/9L mutations. The IBMFS monogenic disorders were first recognized by their phenotype. Exome sequencing has validated their classification, with clusters of gene mutations affecting DNA damage response (Fanconi anemia), ribosome structure (Diamond–Blackfan anemia), ribosome assembly (Shwachman–Diamond syndrome), or telomere maintenance/stability (dyskeratosis congenita). The pathogenetic mechanisms of IBMFSs remain to be characterized fully, but an overarching hypothesis states that different stresses elicit TP53-dependent growth arrest and apoptosis of hematopoietic stem, progenitor, and precursor cells. Here, we review the IBMFSs and propose a role for pro-inflammatory cytokines, such as TGF-β, IL-1β, and IFN-α, in mediating the cytopenias. We suggest a pathogenic role for cytokines in the transformation to myeloid neoplasia and hypothesize a role for anti-inflammatory therapies. Full article

(This article belongs to the Special Issue Regulation of Cytokine Signaling in Health and Disease)

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17 pages, 1341 KiB

Open AccessEditor’s ChoiceArticle

Long-Term Culturing of FreeStyle 293-F Cells Affects Immunoglobulin G Glycome Composition

by Fran Lukšić, Anika Mijakovac, Goran Josipović, Vedrana Vičić Bočkor, Jasminka Krištić, Ana Cindrić, Martina Vinicki, Filip Rokić, Oliver Vugrek, Gordan Lauc and Vlatka Zoldoš

Biomolecules 2023, 13(8), 1245; https://doi.org/10.3390/biom13081245 - 14 Aug 2023

Viewed by 1938

Abstract

Glycosylation of IgG regulates the effector function of this antibody in the immune response. Glycosylated IgG is a potent therapeutic used for both research and clinical purposes. While there is ample research on how different cell culture conditions affect IgG glycosylation, the data [...] Read more.

Glycosylation of IgG regulates the effector function of this antibody in the immune response. Glycosylated IgG is a potent therapeutic used for both research and clinical purposes. While there is ample research on how different cell culture conditions affect IgG glycosylation, the data are missing on the stability of IgG glycome during long cell passaging, i.e., cell “aging”. To test this, we performed three independent time course experiments in FreeStyle 293-F cells, which secrete IgG with a human-like glycosylation pattern and are frequently used to generate defined IgG glycoforms. During long-term cell culturing, IgG glycome stayed fairly stable except for galactosylation, which appeared extremely variable. Cell transcriptome analysis revealed no correlation in galactosyltransferase B4GALT1 expression with galactosylation change, but with expression of EEF1A1 and SLC38A10, genes previously associated with IgG galactosylation through GWAS. The FreeStyle 293-F cell-based system for IgG production is a good model for studies of mechanisms underlying IgG glycosylation, but results from the present study point to the utmost importance of the need to control IgG galactosylation in both in vitro and in vivo systems. This is especially important for improving the production of precisely glycosylated IgG for therapeutic purposes, since IgG galactosylation affects the inflammatory potential of IgG. Full article

(This article belongs to the Special Issue Protein Glycosylation and Human Diseases)

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11 pages, 7420 KiB

Open AccessEditor’s ChoiceArticle

AlphaFold Accurately Predicts the Structure of Ribosomally Synthesized and Post-Translationally Modified Peptide Biosynthetic Enzymes

by Catriona H. Gordon, Emily Hendrix, Yi He and Mark C. Walker

Biomolecules 2023, 13(8), 1243; https://doi.org/10.3390/biom13081243 - 12 Aug 2023

Viewed by 1953

Abstract

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing class of natural products biosynthesized from a genetically encoded precursor peptide. The enzymes that install the post-translational modifications on these peptides have the potential to be useful catalysts in the production of natural-product-like [...] Read more.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing class of natural products biosynthesized from a genetically encoded precursor peptide. The enzymes that install the post-translational modifications on these peptides have the potential to be useful catalysts in the production of natural-product-like compounds and can install non-proteogenic amino acids in peptides and proteins. However, engineering these enzymes has been somewhat limited, due in part to limited structural information on enzymes in the same families that nonetheless exhibit different substrate selectivities. Despite AlphaFold2’s superior performance in single-chain protein structure prediction, its multimer version lacks accuracy and requires high-end GPUs, which are not typically available to most research groups. Additionally, the default parameters of AlphaFold2 may not be optimal for predicting complex structures like RiPP biosynthetic enzymes, due to their dynamic binding and substrate-modifying mechanisms. This study assessed the efficacy of the structure prediction program ColabFold (a variant of AlphaFold2) in modeling RiPP biosynthetic enzymes in both monomeric and dimeric forms. After extensive benchmarking, it was found that there were no statistically significant differences in the accuracy of the predicted structures, regardless of the various possible prediction parameters that were examined, and that with the default parameters, ColabFold was able to produce accurate models. We then generated additional structural predictions for select RiPP biosynthetic enzymes from multiple protein families and biosynthetic pathways. Our findings can serve as a reference for future enzyme engineering complemented by AlphaFold-related tools. Full article

(This article belongs to the Topic Computer-Based Solutions to Investigate Biological- and Health-Related Problems)

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19 pages, 6804 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Hidden Glutathione Transferases in the Human Genome

by Aaron J. Oakley

Biomolecules 2023, 13(8), 1240; https://doi.org/10.3390/biom13081240 - 12 Aug 2023

Cited by 1 | Viewed by 1317

Abstract

With the development of accurate protein structure prediction algorithms, artificial intelligence (AI) has emerged as a powerful tool in the field of structural biology. AI-based algorithms have been used to analyze large amounts of protein sequence data including the human proteome, complementing experimental [...] Read more.

With the development of accurate protein structure prediction algorithms, artificial intelligence (AI) has emerged as a powerful tool in the field of structural biology. AI-based algorithms have been used to analyze large amounts of protein sequence data including the human proteome, complementing experimental structure data found in resources such as the Protein Data Bank. The EBI AlphaFold Protein Structure Database (for example) contains over 230 million structures. In this study, these data have been analyzed to find all human proteins containing (or predicted to contain) the cytosolic glutathione transferase (cGST) fold. A total of 39 proteins were found, including the alpha-, mu-, pi-, sigma-, zeta- and omega-class GSTs, intracellular chloride channels, metaxins, multisynthetase complex components, elongation factor 1 complex components and others. Three broad themes emerge: cGST domains as enzymes, as chloride ion channels and as protein–protein interaction mediators. As the majority of cGSTs are dimers, the AI-based structure prediction algorithm AlphaFold-multimer was used to predict structures of all pairwise combinations of these cGST domains. Potential homo- and heterodimers are described. Experimental biochemical and structure data is used to highlight the strengths and limitations of AI-predicted structures. Full article

(This article belongs to the Special Issue Versatility of Glutathione Transferase Proteins)

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14 pages, 5715 KiB

Open AccessEditor’s ChoiceArticle

Graph-Based Analyses of Dynamic Water-Mediated Hydrogen-Bond Networks in Phosphatidylserine: Cholesterol Membranes

by Honey Jain, Konstantina Karathanou and Ana-Nicoleta Bondar

Biomolecules 2023, 13(8), 1238; https://doi.org/10.3390/biom13081238 - 11 Aug 2023

Cited by 1 | Viewed by 1346

Abstract

Phosphatidylserine lipids are anionic molecules present in eukaryotic plasma membranes, where they have essential physiological roles. The altered distribution of phosphatidylserine in cells such as apoptotic cancer cells, which, unlike healthy cells, expose phosphatidylserine, is of direct interest for the development of biomarkers. [...] Read more.

Phosphatidylserine lipids are anionic molecules present in eukaryotic plasma membranes, where they have essential physiological roles. The altered distribution of phosphatidylserine in cells such as apoptotic cancer cells, which, unlike healthy cells, expose phosphatidylserine, is of direct interest for the development of biomarkers. We present here applications of a recently implemented Depth-First-Search graph algorithm to dissect the dynamics of transient water-mediated lipid clusters at the interface of a model bilayer composed of 1-palmytoyl-2-oleoyl-sn-glycero-2-phosphatidylserine (POPS) and cholesterol. Relative to a reference POPS bilayer without cholesterol, in the POPS:cholesterol bilayer there is a somewhat less frequent sampling of relatively complex and extended water-mediated hydrogen-bond networks of POPS headgroups. The analysis protocol used here is more generally applicable to other lipid:cholesterol bilayers. Full article

(This article belongs to the Special Issue Proton and Proton-Coupled Transport)

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19 pages, 1208 KiB

Open AccessEditor’s ChoiceReview

The Mechanisms of Action of Hyperbaric Oxygen in Restoring Host Homeostasis during Sepsis

by Julie Vinkel, Bjoern Arenkiel and Ole Hyldegaard

Biomolecules 2023, 13(8), 1228; https://doi.org/10.3390/biom13081228 - 7 Aug 2023

Cited by 4 | Viewed by 2363

Abstract

The perception of sepsis has shifted over time; however, it remains a leading cause of death worldwide. Sepsis is now recognized as an imbalance in host cellular functions triggered by the invading pathogens, both related to immune cells, endothelial function, glucose and oxygen [...] Read more.

The perception of sepsis has shifted over time; however, it remains a leading cause of death worldwide. Sepsis is now recognized as an imbalance in host cellular functions triggered by the invading pathogens, both related to immune cells, endothelial function, glucose and oxygen metabolism, tissue repair and restoration. Many of these key mechanisms in sepsis are also targets of hyperbaric oxygen (HBO₂) treatment. HBO₂ treatment has been shown to improve survival in clinical studies on patients with necrotizing soft tissue infections as well as experimental sepsis models. High tissue oxygen tension during HBO₂ treatment may affect oxidative phosphorylation in mitochondria. Oxygen is converted to energy, and, as a natural byproduct, reactive oxygen species are produced. Reactive oxygen species can act as mediators, and both these and the HBO₂-mediated increase in oxygen supply have the potential to influence the cellular processes involved in sepsis. The pathophysiology of sepsis can be explained comprehensively through resistance and tolerance to infection. We argue that HBO₂ treatment may protect the host from collateral tissue damage during resistance by reducing neutrophil extracellular traps, inhibiting neutrophil adhesion to vascular endothelium, reducing proinflammatory cytokines, and halting the Warburg effect, while also assisting the host in tolerance to infection by reducing iron-mediated injury and upregulating anti-inflammatory measures. Finally, we show how inflammation and oxygen-sensing pathways are connected on the cellular level in a self-reinforcing and detrimental manner in inflammatory conditions, and with support from a substantial body of studies from the literature, we conclude by demonstrating that HBO₂ treatment can intervene to maintain homeostasis. Full article

(This article belongs to the Special Issue Advances in Oxygen Therapy with a Special Focus on Immunomodulation and Infection)

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29 pages, 3802 KiB

Open AccessEditor’s ChoiceArticle

The Impact of Viral Infection on the Chemistries of the Earth’s Most Abundant Photosynthesizes: Metabolically Talented Aquatic Cyanobacteria

by Yunpeng Wang, Scarlet Ferrinho, Helen Connaris and Rebecca J. M. Goss

Biomolecules 2023, 13(8), 1218; https://doi.org/10.3390/biom13081218 - 4 Aug 2023

Cited by 2 | Viewed by 1662

Abstract

Cyanobacteria are the most abundant photosynthesizers on earth, and as such, they play a central role in marine metabolite generation, ocean nutrient cycling, and the control of planetary oxygen generation. Cyanobacteriophage infection exerts control on all of these critical processes of the planet, [...] Read more.

Cyanobacteria are the most abundant photosynthesizers on earth, and as such, they play a central role in marine metabolite generation, ocean nutrient cycling, and the control of planetary oxygen generation. Cyanobacteriophage infection exerts control on all of these critical processes of the planet, with the phage-ported homologs of genes linked to photosynthesis, catabolism, and secondary metabolism (marine metabolite generation). Here, we analyze the 153 fully sequenced cyanophages from the National Center for Biotechnology Information (NCBI) database and the 45 auxiliary metabolic genes (AMGs) that they deliver into their hosts. Most of these AMGs are homologs of those found within cyanobacteria and play a key role in cyanobacterial metabolism-encoding proteins involved in photosynthesis, central carbon metabolism, phosphate metabolism, methylation, and cellular regulation. A greater understanding of cyanobacteriophage infection will pave the way to a better understanding of carbon fixation and nutrient cycling, as well as provide new tools for synthetic biology and alternative approaches for the use of cyanobacteria in biotechnology and sustainable manufacturing. Full article

(This article belongs to the Special Issue Marine-Derived Molecules with Different Bioactivities)

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16 pages, 2091 KiB

Open AccessEditor’s ChoiceArticle

Phosphoserine Aminotransferase Pathogenetic Variants in Serine Deficiency Disorders: A Functional Characterization

by Francesco Marchesani, Annalisa Michielon, Elisabetta Viale, Annalisa Bianchera, Davide Cavazzini, Loredano Pollegioni, Giulia Murtas, Andrea Mozzarelli, Stefano Bettati, Alessio Peracchi, Barbara Campanini and Stefano Bruno

Biomolecules 2023, 13(8), 1219; https://doi.org/10.3390/biom13081219 - 4 Aug 2023

Cited by 1 | Viewed by 1139

Abstract

In humans, the phosphorylated pathway (PP) converts the glycolytic intermediate D-3-phosphoglycerate (3-PG) into L-serine through the enzymes 3-phosphoglycerate dehydrogenase, phosphoserine aminotransferase (PSAT) and phosphoserine phosphatase. From the pathogenic point of view, the PP in the brain is particularly relevant, as genetic defects of [...] Read more.

In humans, the phosphorylated pathway (PP) converts the glycolytic intermediate D-3-phosphoglycerate (3-PG) into L-serine through the enzymes 3-phosphoglycerate dehydrogenase, phosphoserine aminotransferase (PSAT) and phosphoserine phosphatase. From the pathogenic point of view, the PP in the brain is particularly relevant, as genetic defects of any of the three enzymes are associated with a group of neurometabolic disorders known as serine deficiency disorders (SDDs). We recombinantly expressed and characterized eight variants of PSAT associated with SDDs and two non-SDD associated variants. We show that the pathogenetic mechanisms in SDDs are extremely diverse, including low affinity of the cofactor pyridoxal 5′-phosphate and thermal instability for S179L and G79W PSAT, loss of activity of the holo form for R342W PSAT, aggregation for D100A PSAT, increased K_m for one of the substrates with invariant k_cats for S43R PSAT, and a combination of increased K_m and decreased k_cat for C245R PSAT. Finally, we show that the flux through the in vitro reconstructed PP at physiological concentrations of substrates and enzymes is extremely sensitive to alterations of the functional properties of PSAT variants, confirming PSAT dysfunctions as a cause of SSDs. Full article

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

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14 pages, 35695 KiB

Open AccessEditor’s ChoiceArticle

Del1 Is a Growth Factor for Skeletal Progenitor Cells in the Fracture Callus

by Yuxi Sun, Tatiana Boyko, Owen Marecic, Danielle Struck, Randall K. Mann, Tom W. Andrew, Michael Lopez, Xinming Tong, Stuart B. Goodman, Fan Yang, Michael T. Longaker, Charles K. F. Chan and George P. Yang

Biomolecules 2023, 13(8), 1214; https://doi.org/10.3390/biom13081214 - 3 Aug 2023

Viewed by 1696

Abstract

Failure to properly form bone or integrate surgical implants can lead to morbidity and additional surgical interventions in a significant proportion of orthopedic surgeries. While the role of skeletal stem cells (SSCs) in bone formation and repair is well-established, very little is known [...] Read more.

Failure to properly form bone or integrate surgical implants can lead to morbidity and additional surgical interventions in a significant proportion of orthopedic surgeries. While the role of skeletal stem cells (SSCs) in bone formation and repair is well-established, very little is known about the factors that regulate the downstream Bone, Cartilage, Stromal, Progenitors (BCSPs). BCSPs, as transit amplifying progenitor cells, undergo multiple mitotic divisions to expand the pool of lineage committed progenitors allowing stem cells to preserve their self-renewal and stemness. Del1 is a protein widely expressed in the skeletal system, but its deletion led to minimal phenotype changes in the uninjured mouse. In this paper, we demonstrate that Del1 is a key regulator of BCSP expansion following injury. In Del1 knockout mice, there is a significant reduction in the number of BCSPs which leads to a smaller callus and decreased bone formation compared with wildtype (WT) littermates. Del1 serves to promote BCSP proliferation and prevent apoptosis in vivo and in vitro. Moreover, exogenous Del1 promotes proliferation of aged human BCSPs. Our results highlight the potential of Del1 as a therapeutic target for improving bone formation and implant success. Del1 injections may improve the success of orthopedic surgeries and fracture healing by enhancing the proliferation and survival of BCSPs, which are crucial for generating new bone tissue during the process of bone formation and repair. Full article

(This article belongs to the Topic Bone-Related Diseases: From Molecular Mechanisms to Therapy Development)

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19 pages, 2480 KiB

Open AccessEditor’s ChoiceArticle

A Combination of Conformation-Specific RAF Inhibitors Overcome Drug Resistance Brought about by RAF Overexpression

by Hiroaki Imoto, Nora Rauch, Ashish J. Neve, Fahimeh Khorsand, Martina Kreileder, Leonidas G. Alexopoulos, Jens Rauch, Mariko Okada, Boris N. Kholodenko and Oleksii S. Rukhlenko

Biomolecules 2023, 13(8), 1212; https://doi.org/10.3390/biom13081212 - 2 Aug 2023

Cited by 1 | Viewed by 2472

Abstract

Cancer cells often adapt to targeted therapies, yet the molecular mechanisms underlying adaptive resistance remain only partially understood. Here, we explore a mechanism of RAS/RAF/MEK/ERK (MAPK) pathway reactivation through the upregulation of RAF isoform (RAFs) abundance. Using computational modeling and in vitro experiments, [...] Read more.

Cancer cells often adapt to targeted therapies, yet the molecular mechanisms underlying adaptive resistance remain only partially understood. Here, we explore a mechanism of RAS/RAF/MEK/ERK (MAPK) pathway reactivation through the upregulation of RAF isoform (RAFs) abundance. Using computational modeling and in vitro experiments, we show that the upregulation of RAFs changes the concentration range of paradoxical pathway activation upon treatment with conformation-specific RAF inhibitors. Additionally, our data indicate that the signaling output upon loss or downregulation of one RAF isoform can be compensated by overexpression of other RAF isoforms. We furthermore demonstrate that, while single RAF inhibitors cannot efficiently inhibit ERK reactivation caused by RAF overexpression, a combination of two structurally distinct RAF inhibitors synergizes to robustly suppress pathway reactivation. Full article

(This article belongs to the Special Issue MAP Kinases: Functions in Signal Transduction and Disease)

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16 pages, 9406 KiB

Open AccessEditor’s ChoiceArticle

CXCL10 Is Associated with Increased Cerebrospinal Fluid Immune Cell Infiltration and Disease Duration in Multiple Sclerosis

by Stephanie N. Blandford, Neva J. Fudge and Craig S. Moore

Biomolecules 2023, 13(8), 1204; https://doi.org/10.3390/biom13081204 - 1 Aug 2023

Cited by 3 | Viewed by 1518

Abstract

Background: Cerebrospinal fluid (CSF) is an important sampling site for putative biomarkers and contains immune cells. CXCL10 is a multiple sclerosis (MS)-relevant chemokine that is present in the injured central nervous system and recruits CXCR3+ immune cells toward injured tissues. Objective: Perform a [...] Read more.

Background: Cerebrospinal fluid (CSF) is an important sampling site for putative biomarkers and contains immune cells. CXCL10 is a multiple sclerosis (MS)-relevant chemokine that is present in the injured central nervous system and recruits CXCR3+ immune cells toward injured tissues. Objective: Perform a comprehensive evaluation to determine a potential relationship between CXCL10 and various immune cell subsets in the CNS of MS and control cases. Methods: In MS and control cases, CXCL10 was measured in the CSF and plasma by ELISA. Immune cells within both the CSF and peripheral blood were quantified by flow cytometry. Results: Compared to non-inflammatory neurological disease (NIND) cases, MS cases had significantly higher CXCL10 in CSF (p = 0.021); CXCL10 was also correlated with total cell numbers in CSF (p = 0.04) and T cell infiltrates (CD3+, p = 0.01; CD4+, p = 0.01; CD8+, p = 0.02); expression of CXCR3 on peripheral immune cell subsets was not associated with CSF CXCL10. Conclusions: Elevated levels of CXCL10 in the CSF of MS cases are associated with increased T cells but appear to be independent of peripheral CXCR3 expression. These results support the importance of elevated CXCL10 in MS and suggest the presence of an alternative mechanism of CXCL10 outside of solely influencing immune cell trafficking. Full article

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

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20 pages, 938 KiB

Open AccessEditor’s ChoiceReview

Challenges and Opportunities in Developing Targeted Therapies for Triple Negative Breast Cancer

by Abygail G. Chapdelaine and Gongqin Sun

Biomolecules 2023, 13(8), 1207; https://doi.org/10.3390/biom13081207 - 1 Aug 2023

Cited by 8 | Viewed by 2835

Abstract

Triple negative breast cancer (TNBC) is a heterogeneous group of breast cancers characterized by their lack of estrogen receptors, progesterone receptors, and the HER2 receptor. They are more aggressive than other breast cancer subtypes, with a higher mean tumor size, higher tumor grade, [...] Read more.

Triple negative breast cancer (TNBC) is a heterogeneous group of breast cancers characterized by their lack of estrogen receptors, progesterone receptors, and the HER2 receptor. They are more aggressive than other breast cancer subtypes, with a higher mean tumor size, higher tumor grade, the worst five-year overall survival, and the highest rates of recurrence and metastasis. Developing targeted therapies for TNBC has been a major challenge due to its heterogeneity, and its treatment still largely relies on surgery, radiation therapy, and chemotherapy. In this review article, we review the efforts in developing targeted therapies for TNBC, discuss insights gained from these efforts, and highlight potential opportunities going forward. Accumulating evidence supports TNBCs as multi-driver cancers, in which multiple oncogenic drivers promote cell proliferation and survival. In such multi-driver cancers, targeted therapies would require drug combinations that simultaneously block multiple oncogenic drivers. A strategy designed to generate mechanism-based combination targeted therapies for TNBC is discussed. Full article

(This article belongs to the Special Issue Molecular Targets for Breast Cancer Therapy)

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22 pages, 1526 KiB

Open AccessEditor’s ChoiceReview

Chronic Hepatitis B Infection: New Approaches towards Cure

by Mojisola Ogunnaike, Srijanee Das, Samiksha S. Raut, Ashrafi Sultana, Mohammad Ullah Nayan, Murali Ganesan, Benson J. Edagwa, Natalia A. Osna and Larisa Y. Poluektova

Biomolecules 2023, 13(8), 1208; https://doi.org/10.3390/biom13081208 - 1 Aug 2023

Cited by 4 | Viewed by 6104

Abstract

Chronic hepatitis B virus (HBV) infection leads to the development of cirrhosis and hepatocellular carcinoma. Lifelong treatment with nucleotides/nucleoside antiviral agents is effective at suppressing HBV replication, however, adherence to daily therapy can be challenging. This review discusses recent advances in the development [...] Read more.

Chronic hepatitis B virus (HBV) infection leads to the development of cirrhosis and hepatocellular carcinoma. Lifelong treatment with nucleotides/nucleoside antiviral agents is effective at suppressing HBV replication, however, adherence to daily therapy can be challenging. This review discusses recent advances in the development of long-acting formulations for HBV treatment and prevention, which could potentially improve adherence. Promising new compounds that target distinct steps of the virus life cycle are summarized. In addition to treatments that suppress viral replication, curative strategies are focused on the elimination of covalently closed circular DNA and the inactivation of the integrated viral DNA from infected hepatocytes. We highlight promising long-acting antivirals and genome editing strategies for the elimination or deactivation of persistent viral DNA products in development. Full article

(This article belongs to the Special Issue Targets and Treatment Approaches for End-Stage Liver Diseases)

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22 pages, 2209 KiB

Open AccessEditor’s ChoiceReview

Role of Mitochondria–ER Contact Sites in Mitophagy

by Alina Rühmkorf and Angelika Bettina Harbauer

Biomolecules 2023, 13(8), 1198; https://doi.org/10.3390/biom13081198 - 31 Jul 2023

Cited by 5 | Viewed by 2684

Abstract

Mitochondria are often referred to as the “powerhouse” of the cell. However, this organelle has many more functions than simply satisfying the cells’ metabolic needs. Mitochondria are involved in calcium homeostasis and lipid metabolism, and they also regulate apoptotic processes. Many of these [...] Read more.

Mitochondria are often referred to as the “powerhouse” of the cell. However, this organelle has many more functions than simply satisfying the cells’ metabolic needs. Mitochondria are involved in calcium homeostasis and lipid metabolism, and they also regulate apoptotic processes. Many of these functions require contact with the ER, which is mediated by several tether proteins located on the respective organellar surfaces, enabling the formation of mitochondria–ER contact sites (MERCS). Upon damage, mitochondria produce reactive oxygen species (ROS) that can harm the surrounding cell. To circumvent toxicity and to maintain a functional pool of healthy organelles, damaged and excess mitochondria can be targeted for degradation via mitophagy, a form of selective autophagy. Defects in mitochondria–ER tethers and the accumulation of damaged mitochondria are found in several neurodegenerative diseases, including Parkinson’s disease and amyotrophic lateral sclerosis, which argues that the interplay between the two organelles is vital for neuronal health. This review provides an overview of the different mechanisms of mitochondrial quality control that are implicated with the different mitochondria–ER tether proteins, and also provides a novel perspective on how MERCS are involved in mediating mitophagy upon mitochondrial damage. Full article

(This article belongs to the Special Issue Mitochondrial Quality Control in Aging and Neurodegeneration)

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17 pages, 3410 KiB

Open AccessEditor’s ChoiceArticle

Serum Soluble Lectin-like Oxidized Low-Density Lipoprotein Receptor-1 (sLOX-1) Is Associated with Atherosclerosis Severity in Coronary Artery Disease

by Katharine A. Kott, Elijah Genetzakis, Michael P. Gray, Peter Hansen, Helen M. McGuire, Jean Y. Yang, Stuart M. Grieve, Stephen T. Vernon and Gemma A. Figtree

Biomolecules 2023, 13(8), 1187; https://doi.org/10.3390/biom13081187 - 29 Jul 2023

Viewed by 1246

Abstract

Risk-factor-based scoring systems for atherosclerotic coronary artery disease (CAD) remain concerningly inaccurate at the level of the individual and would benefit from the addition of biomarkers that correlate with atherosclerosis burden directly. We hypothesized that serum soluble lectin-like oxidized low-density lipoprotein receptor-1 (sLOX-1) [...] Read more.

Risk-factor-based scoring systems for atherosclerotic coronary artery disease (CAD) remain concerningly inaccurate at the level of the individual and would benefit from the addition of biomarkers that correlate with atherosclerosis burden directly. We hypothesized that serum soluble lectin-like oxidized low-density lipoprotein receptor-1 (sLOX-1) would be independently associated with CAD and investigated this in the BioHEART study using 968 participants with CT coronary angiograms, which were scored for disease burden in the form of coronary artery calcium scores (CACS), Gensini scores, and a semi-quantitative soft-plaque score (SPS). Serum sLOX-1 was assessed by ELISA and was incorporated into regression models for disease severity and incidence. We demonstrate that sLOX-1 is associated with an improvement in the prediction of CAD severity when scored by Gensini or SPS, but not CACS. sLOX-1 also significantly improved the prediction of the incidence of obstructive CAD, defined as stenosis in any vessel >75%. The predictive value of sLOX-1 was significantly greater in the subgroup of patients who did not have any of the standard modifiable cardiovascular risk factors (SMuRFs). sLOX-1 is associated with CAD severity and is the first biomarker shown to have utility for risk prediction in the SMuRFless population. Full article

(This article belongs to the Special Issue Cardiovascular Diseases and Biomarkers)

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21 pages, 3365 KiB

Open AccessEditor’s ChoiceArticle

Hemocompatibility of β-Cyclodextrin-Modified (Methacryloyloxy)ethyl Phosphorylcholine Coated Magnetic Nanoparticles

by Shuhui Li, Mehdi Ghaffari Sharaf, Elyn M. Rowe, Katherine Serrano, Dana V. Devine and Larry D. Unsworth

Biomolecules 2023, 13(8), 1165; https://doi.org/10.3390/biom13081165 - 25 Jul 2023

Viewed by 1388

Abstract

Adsorbing toxins from the blood to augment membrane-based hemodialysis is an active area of research. Films composed of β-cyclodextrin-co-(methacryloyloxy)ethyl phosphorylcholine (p(PMβCD-co-MPC)) with various monomer ratios were formed on magnetic nanoparticles and characterized. Surface chemistry effects on protein denaturation were evaluated and indicated that [...] Read more.

Adsorbing toxins from the blood to augment membrane-based hemodialysis is an active area of research. Films composed of β-cyclodextrin-co-(methacryloyloxy)ethyl phosphorylcholine (p(PMβCD-co-MPC)) with various monomer ratios were formed on magnetic nanoparticles and characterized. Surface chemistry effects on protein denaturation were evaluated and indicated that unmodified magnetic nanoparticles greatly perturbed the structure of proteins compared to coated particles. Plasma clotting assays were conducted to investigate the stability of plasma in the presence of particles, where a 2:2 monomer ratio yielded the best results for a given total surface area of particles. Total protein adsorption results revealed that modified surfaces exhibited reduced protein adsorption compared to bare particles, and pure MPC showed the lowest adsorption. Immunoblot results showed that fibrinogen, α1-antitrypsin, vitronectin, prekallikrein, antithrombin, albumin, and C3 correlated with film composition. Hemocompatibility testing with whole blood illustrated that the 1:3 ratio of CD to MPC had a negative impact on platelets, as evidenced by the increased activation, reduced response to an agonist, and reduced platelet count. Other formulations had statistically significant effects on platelet activation, but no formulation yielded apparent adverse effects on hemostasis. For the first time, p(PMβCD-co-MPC)-coated MNP were synthesized and their general hemocompatibility assessed. Full article

(This article belongs to the Special Issue Mechanisms and Kinetics of Interactions of Biomolecules at Interfaces)

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17 pages, 3567 KiB

Open AccessEditor’s ChoiceArticle

Goldilocks Dilemma: LPS Works Both as the Initial Target and a Barrier for the Antimicrobial Action of Cationic AMPs on E. coli

by Martin Jakubec, Fredrik G. Rylandsholm, Philip Rainsford, Mitchell Silk, Maxim Bril’kov, Tone Kristoffersen, Eric Juskewitz, Johanna U. Ericson and John Sigurd M. Svendsen

Biomolecules 2023, 13(7), 1155; https://doi.org/10.3390/biom13071155 - 20 Jul 2023

Cited by 5 | Viewed by 1985

Abstract

Antimicrobial peptides (AMPs) are generally membrane-active compounds that physically disrupt bacterial membranes. Despite extensive research, the precise mode of action of AMPs is still a topic of great debate. This work demonstrates that the initial interaction between the Gram-negative E. coli and AMPs [...] Read more.

Antimicrobial peptides (AMPs) are generally membrane-active compounds that physically disrupt bacterial membranes. Despite extensive research, the precise mode of action of AMPs is still a topic of great debate. This work demonstrates that the initial interaction between the Gram-negative E. coli and AMPs is driven by lipopolysaccharides (LPS) that act as kinetic barriers for the binding of AMPs to the bacterial membrane. A combination of SPR and NMR experiments provide evidence suggesting that cationic AMPs first bind to the negatively charged LPS before reaching a binding place in the lipid bilayer. In the event that the initial LPS-binding is too strong (corresponding to a low dissociation rate), the cationic AMPs cannot effectively get from the LPS to the membrane, and their antimicrobial potency will thus be diminished. On the other hand, the AMPs must also be able to effectively interact with the membrane to exert its activity. The ability of the studied cyclic hexapeptides to bind LPS and to translocate into a lipid membrane is related to the nature of the cationic charge (arginine vs. lysine) and to the distribution of hydrophobicity along the molecule (alternating vs. clumped tryptophan). Full article

(This article belongs to the Special Issue Mechanisms and Kinetics of Interactions of Biomolecules at Interfaces)

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32 pages, 4133 KiB

Open AccessEditor’s ChoiceReview

A Frame-by-Frame Glance at Membrane Fusion Mechanisms: From Viral Infections to Fertilization

by Farshad C. Azimi, Trevor T. Dean, Karine Minari, Luis G. M. Basso, Tyler D. R. Vance and Vitor Hugo B. Serrão

Biomolecules 2023, 13(7), 1130; https://doi.org/10.3390/biom13071130 - 14 Jul 2023

Cited by 3 | Viewed by 2429

Abstract

Viral entry and fertilization are distinct biological processes that share a common mechanism: membrane fusion. In viral entry, enveloped viruses attach to the host cell membrane, triggering a series of conformational changes in the viral fusion proteins. This results in the exposure of [...] Read more.

Viral entry and fertilization are distinct biological processes that share a common mechanism: membrane fusion. In viral entry, enveloped viruses attach to the host cell membrane, triggering a series of conformational changes in the viral fusion proteins. This results in the exposure of a hydrophobic fusion peptide, which inserts into the host membrane and brings the viral and host membranes into close proximity. Subsequent structural rearrangements in opposing membranes lead to their fusion. Similarly, membrane fusion occurs when gametes merge during the fertilization process, though the exact mechanism remains unclear. Structural biology has played a pivotal role in elucidating the molecular mechanisms underlying membrane fusion. High-resolution structures of the viral and fertilization fusion-related proteins have provided valuable insights into the conformational changes that occur during this process. Understanding these mechanisms at a molecular level is essential for the development of antiviral therapeutics and tools to influence fertility. In this review, we will highlight the biological importance of membrane fusion and how protein structures have helped visualize both common elements and subtle divergences in the mechanisms behind fusion; in addition, we will examine the new tools that recent advances in structural biology provide researchers interested in a frame-by-frame understanding of membrane fusion. Full article

(This article belongs to the Special Issue Molecular Mechanism Investigations into Membrane Fusion)

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23 pages, 14523 KiB

Open AccessEditor’s ChoiceArticle

A Molecular Analysis of the Aminopeptidase P-Related Domain of PID-5 from Caenorhabditis elegans

by Anna C. Lloyd, Kyle S. Gregory, R. Elwyn Isaac and K. Ravi Acharya

Biomolecules 2023, 13(7), 1132; https://doi.org/10.3390/biom13071132 - 14 Jul 2023

Cited by 1 | Viewed by 1698

Abstract

A novel protein, PID-5, has been shown to be a requirement for germline immortality and has recently been implicated in RNA-induced epigenetic silencing in the Caenorhabditis elegans embryo. Importantly, it has been shown to contain both an eTudor and aminopeptidase P-related domain. However, [...] Read more.

A novel protein, PID-5, has been shown to be a requirement for germline immortality and has recently been implicated in RNA-induced epigenetic silencing in the Caenorhabditis elegans embryo. Importantly, it has been shown to contain both an eTudor and aminopeptidase P-related domain. However, the silencing mechanism has not yet been fully characterised. In this study, bioinformatic tools were used to compare pre-existing aminopeptidase P molecular structures to the AlphaFold2-predicted aminopeptidase P-related domain of PID-5 (PID-5 APP-RD). Structural homology, metal composition, inhibitor-bonding interactions, and the potential for dimerisation were critically assessed through computational techniques, including structural superimposition and protein-ligand docking. Results from this research suggest that the metallopeptidase-like domain shares high structural homology with known aminopeptidase P enzymes and possesses the canonical ‘pita-bread fold’. However, the absence of conserved metal-coordinating residues indicates that only a single Zn²⁺ may be bound at the active site. The PID-5 APP-RD may form transient interactions with a known aminopeptidase P inhibitor and may therefore recognise substrates in a comparable way to the known structures. However, loss of key catalytic residues suggests the domain will be inactive. Further evidence suggests that heterodimerisation with C. elegans aminopeptidase P is feasible and therefore PID-5 is predicted to regulate proteolytic cleavage in the silencing pathway. PID-5 may interact with PID-2 to bring aminopeptidase P activity to the Z-granule, where it could influence WAGO-4 activity to ensure the balanced production of 22G-RNA signals for transgenerational silencing. Targeted experiments into APPs implicated in malaria and cancer are required in order to build upon the biological and therapeutic significance of this research. Full article

(This article belongs to the Topic Metalloproteins and Metalloenzymes)

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11 pages, 5442 KiB

Open AccessEditor’s ChoiceArticle

Design of Beta-2 Microglobulin Adsorbent Protein Nanoparticles

by Justin E. Miller, Roger Castells-Graells, Mark A. Arbing, Aldo Munoz, Yi-Xiao Jiang, Charlize T. Espinoza, Brian Nguyen, Paul Moroz and Todd O. Yeates

Biomolecules 2023, 13(7), 1122; https://doi.org/10.3390/biom13071122 - 14 Jul 2023

Cited by 5 | Viewed by 1923

Abstract

Beta-2 microglobulin (B2M) is an immune system protein that is found on the surface of all nucleated human cells. B2M is naturally shed from cell surfaces into the plasma, followed by renal excretion. In patients with impaired renal function, B2M will accumulate in [...] Read more.

Beta-2 microglobulin (B2M) is an immune system protein that is found on the surface of all nucleated human cells. B2M is naturally shed from cell surfaces into the plasma, followed by renal excretion. In patients with impaired renal function, B2M will accumulate in organs and tissues leading to significantly reduced life expectancy and quality of life. While current hemodialysis methods have been successful in managing electrolyte as well as small and large molecule disturbances arising in chronic renal failure, they have shown only modest success in managing plasma levels of B2M and similar sized proteins, while sparing important proteins such as albumin. We describe a systematic protein design effort aimed at adding the ability to selectively remove specific, undesired waste proteins such as B2M from the plasma of chronic renal failure patients. A novel nanoparticle built using a tetrahedral protein assembly as a scaffold that presents 12 copies of a B2M-binding nanobody is described. The designed nanoparticle binds specifically to B2M through protein–protein interactions with nanomolar binding affinity (~4.2 nM). Notably, binding to the nanoparticle increases the effective size of B2M by over 50-fold, offering a potential selective avenue for separation based on size. We present data to support the potential utility of such a nanoparticle for removing B2M from plasma by either size-based filtration or by polyvalent binding to a stationary matrix under blood flow conditions. Such applications could address current shortcomings in the management of problematic mid-sized proteins in chronic renal failure patients. Full article

(This article belongs to the Section Biomacromolecules: Proteins)

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10 pages, 1211 KiB

Open AccessEditor’s ChoiceArticle

An Integrated Glycosylation Signature of Rheumatoid Arthritis

by Oleg A. Mayboroda, Guinevere S. M. Lageveen-Kammeijer, Manfred Wuhrer and Radboud J. E. M. Dolhain

Biomolecules 2023, 13(7), 1106; https://doi.org/10.3390/biom13071106 - 12 Jul 2023

Viewed by 1296

Abstract

Rheumatoid arthritis (RA) Is a highly prevalent autoimmune disease that affects the joints but also various other organs. The disease is characterized by autoantibodies that are often already observed pre-disease. Since the 1980s, it has been known that antibody glycosylation is different in [...] Read more.

Rheumatoid arthritis (RA) Is a highly prevalent autoimmune disease that affects the joints but also various other organs. The disease is characterized by autoantibodies that are often already observed pre-disease. Since the 1980s, it has been known that antibody glycosylation is different in RA as compared to control individuals. While the literature on glycosylation changes in RA is dominated by reports on serum or plasma immunoglobulin G (IgG), our recent studies have indicated that the glycosylation changes observed for immunoglobulin A (IgA) and total serum N-glycome (TSNG) may be similarly prominent, and useful in differentiating between the RA patients and controls, or as a proxy of the disease activity. In this study, we integrated and compared the RA glycosylation signatures of IgG, IgA and TSNG, all determined in the pregnancy-induced amelioration of rheumatoid arthritis (PARA) cohort. We assessed the association of the altered glycosylation patterns with the disease, autoantibody positivity and disease activity. Our analyses indicated a common, composite glycosylation signature of RA that was independent of the autoantibody status. Full article

(This article belongs to the Special Issue Protein Glycosylation and Human Diseases)

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22 pages, 3658 KiB

Open AccessEditor’s ChoiceArticle

The Metallodrug BOLD-100 Is a Potent Inhibitor of SARS-CoV-2 Replication and Has Broad-Acting Antiviral Activity

by Daniel S. Labach, Hinissan P. Kohio, Edwin A. Tse, Ermela Paparisto, Nicole J. Friesen, Jim Pankovich, Mark Bazett and Stephen D. Barr

Biomolecules 2023, 13(7), 1095; https://doi.org/10.3390/biom13071095 - 8 Jul 2023

Cited by 3 | Viewed by 1847

Abstract

The COVID-19 pandemic has highlighted an urgent need to discover and test new drugs to treat patients. Metal-based drugs are known to interact with DNA and/or a variety of proteins such as enzymes and transcription factors, some of which have been shown to [...] Read more.

The COVID-19 pandemic has highlighted an urgent need to discover and test new drugs to treat patients. Metal-based drugs are known to interact with DNA and/or a variety of proteins such as enzymes and transcription factors, some of which have been shown to exhibit anticancer and antimicrobial effects. BOLD-100 (sodium trans-[tetrachlorobis(1H-indazole)ruthenate(III)]dihydrate) is a novel ruthenium-based drug currently being evaluated in a Phase 1b/2a clinical trial for the treatment of advanced gastrointestinal cancer. Given that metal-based drugs are known to exhibit antimicrobial activities, we asked if BOLD-100 exhibits antiviral activity towards SARS-CoV-2. We demonstrated that BOLD-100 potently inhibits SARS-CoV-2 replication and cytopathic effects in vitro. An RNA sequencing analysis showed that BOLD-100 inhibits virus-induced transcriptional changes in infected cells. In addition, we showed that the antiviral activity of BOLD-100 is not specific for SARS-CoV-2, but also inhibits the replication of the evolutionarily divergent viruses Human Immunodeficiency Virus type 1 and Human Adenovirus type 5. This study identifies BOLD-100 as a potentially novel broad-acting antiviral drug. Full article

(This article belongs to the Special Issue Viral Drug Targets and Discovery of Antiviral Agents)

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23 pages, 1444 KiB

Open AccessEditor’s ChoiceArticle

Xanthine–Dopamine Hybrid Molecules as Multitarget Drugs with Potential for the Treatment of Neurodegenerative Diseases

by Michał Załuski, Tadeusz Karcz, Anna Drabczyńska, Christin Vielmuth, Agnieszka Olejarz-Maciej, Monika Głuch-Lutwin, Barbara Mordyl, Agata Siwek, Grzegorz Satała, Christa E. Müller and Katarzyna Kieć-Kononowicz

Biomolecules 2023, 13(7), 1079; https://doi.org/10.3390/biom13071079 - 5 Jul 2023

Cited by 3 | Viewed by 1765

Abstract

Multitarget drugs based on a hybrid dopamine–xanthine core were designed as potential drug candidates for the treatment of neurodegenerative diseases. Monoamine oxidase B (MAO-B) inhibitors with significant ancillary A_2A adenosine receptor (A_2AAR) antagonistic properties were further developed to exhibit additional [...] Read more.

Multitarget drugs based on a hybrid dopamine–xanthine core were designed as potential drug candidates for the treatment of neurodegenerative diseases. Monoamine oxidase B (MAO-B) inhibitors with significant ancillary A_2A adenosine receptor (A_2AAR) antagonistic properties were further developed to exhibit additional phosphodiesterase-4 and -10 (PDE4/10) inhibition and/or dopamine D₂ receptor (D₂R) agonistic activity. While all of the designed compounds showed MAO-B inhibition in the nanomolar range mostly combined with submicromolar A_2AAR affinity, significant enhancement of PDE-inhibitory and D₂R-agonistic activity was additionally reached for some compounds through various structural modifications. The final multitarget drugs also showed promising antioxidant properties in vitro. In order to evaluate their potential neuroprotective effect, representative ligands were tested in a cellular model of toxin-induced neurotoxicity. As a result, protective effects against oxidative stress in neuroblastoma cells were observed, confirming the utility of the applied strategy. Further evaluation of the newly developed multitarget ligands in preclinical models of Alzheimer’s and Parkinson’s diseases is warranted. Full article

(This article belongs to the Special Issue Current Progress in Protein Studies in the Context of Civilization Problems: From In Silico to In Vivo)

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18 pages, 2548 KiB

Open AccessEditor’s ChoiceArticle

Activation of Metabotropic Glutamate Receptor (mGlu₂) and Muscarinic Receptors (M₁, M₄, and M₅), Alone or in Combination, and Its Impact on the Acquisition and Retention of Learning in the Morris Water Maze, NMDA Expression and cGMP Synthesis

by Joanna M. Wierońska, Paulina Cieślik, Grzegorz Burnat and Leszek Kalinowski

Biomolecules 2023, 13(7), 1064; https://doi.org/10.3390/biom13071064 - 30 Jun 2023

Cited by 4 | Viewed by 1657

Abstract

The Morris water maze (MWM) is regarded as one of the most popular tests for detecting spatial memory in rodents. Long-term potentiation and cGMP synthesis seem to be among the crucial factors involved in this type of learning. Muscarinic (M₁, M [...] Read more.

The Morris water maze (MWM) is regarded as one of the most popular tests for detecting spatial memory in rodents. Long-term potentiation and cGMP synthesis seem to be among the crucial factors involved in this type of learning. Muscarinic (M₁, M₄, and M₅ receptors) and metabotropic glutamate (mGlu) receptors are important targets in the search for antipsychotic drugs with the potency to treat cognitive disabilities associated with the disorder. Here, we show that muscarinic receptor activators (VU0357017, VU0152100, and VU0238429) and an mGlu₂ receptor activator, LY487379, dose-dependently prevented the development of cognitive disorders as a result of MK-801 administration in the MWM. The dose-ranges of the compounds were as follows: VU0357017, 0.25, 0.5, and 1 mg/kg; VU0152100, 0.05, 0.25, and 1 mg/kg; VU0238429, 1, 5, and 20 mg/kg; and LY487379, 0.5, 3, and 5 mg/kg. The co-administration of LY487379 with each of the individual muscarinic receptor ligands showed no synergistic effect, which contradicts the results obtained earlier in the novel object recognition (NOR) test. MWM learning resulted in increased cGMP synthesis, both in the cortex and hippocampi, when compared to that in intact animals, which was prevented by MK-801 administration. The investigated compounds at the highest doses reversed this MK-801-induced effect. Neither the procedure nor the treatment resulted in changes in GluN2B-NMDA expression. Full article

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

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23 pages, 9441 KiB

Open AccessEditor’s ChoiceArticle

Quantitative Spatial Analysis of Neuroligin-3 mRNA Expression in the Enteric Nervous System Reveals a Potential Role in Neuronal–Glial Synapses and Reduced Expression in Nlgn3^R451C Mice

by Madushani Herath, Ellie Cho, Ulrika Marklund, Ashley E. Franks, Joel C. Bornstein and Elisa L. Hill-Yardin

Biomolecules 2023, 13(7), 1063; https://doi.org/10.3390/biom13071063 - 30 Jun 2023

Cited by 3 | Viewed by 1781

Abstract

Mutations in the Neuroligin-3 (Nlgn3) gene are implicated in autism spectrum disorder (ASD) and gastrointestinal (GI) dysfunction, but cellular Nlgn3 expression in the enteric nervous system remains to be characterised. We combined RNAScope in situ hybridization and immunofluorescence to measure Nlgn3 [...] Read more.

Mutations in the Neuroligin-3 (Nlgn3) gene are implicated in autism spectrum disorder (ASD) and gastrointestinal (GI) dysfunction, but cellular Nlgn3 expression in the enteric nervous system remains to be characterised. We combined RNAScope in situ hybridization and immunofluorescence to measure Nlgn3 mRNA expression in cholinergic and VIP-expressing submucosal neurons, nitrergic and calretinin-containing myenteric neurons and glial cells in both WT and Nlgn3^R451C mutant mice. We measured Nlgn3 mRNA neuronal and glial expression via quantitative three-dimensional image analysis. To validate dual RNAScope/immunofluorescence data, we interrogated available single-cell RNA sequencing (scRNASeq) data to assess for Nlgn3, Nlgn1, Nlgn2 and their binding partners, Nrxn1-3, MGDA1 and MGDA2, in enteric neural subsets. Most submucosal and myenteric neurons expressed Nlgn3 mRNA. In contrast to other Nlgns and binding partners, Nlgn3 was strongly expressed in enteric glia, suggesting a role for neuroligin-3 in mediating enteric neuron–glia interactions. The autism-associated R451C mutation reduces Nlgn3 mRNA expression in cholinergic but not in VIPergic submucosal neurons. In the myenteric plexus, Nlgn3 mRNA levels are reduced in calretinin, nNOS-labelled neurons and S100 β -labelled glia. We provide a comprehensive cellular profile for neuroligin-3 expression in ileal neuronal subpopulations of mice expressing the R451C autism-associated mutation in Nlgn3, which may contribute to the understanding of the pathophysiology of GI dysfunction in ASD. Full article

(This article belongs to the Special Issue Neuroimmune Interactions in Neuropsychiatric Diseases)

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23 pages, 4070 KiB

Open AccessEditor’s ChoiceArticle

Bioinspired Synthesis of Silver Nanoparticles for the Remediation of Toxic Pollutants and Enhanced Antibacterial Activity

by Sujata Mandal, Sangchul Hwang, Sreekar B. Marpu, Mohammad A. Omary, Victor Prybutok and Sheldon Q. Shi

Biomolecules 2023, 13(7), 1054; https://doi.org/10.3390/biom13071054 - 29 Jun 2023

Cited by 5 | Viewed by 1666

Abstract

This research presents a novel and environmentally friendly approach for the synthesis of multifunctional nanobiocomposites for the efficient removal of toxic heavy metal and dye, as well as the disinfection of wastewater microorganisms. The nanobiocomposites (KAC-CS-AgNPs) were prepared by incorporating photochemically generated silver [...] Read more.

This research presents a novel and environmentally friendly approach for the synthesis of multifunctional nanobiocomposites for the efficient removal of toxic heavy metal and dye, as well as the disinfection of wastewater microorganisms. The nanobiocomposites (KAC-CS-AgNPs) were prepared by incorporating photochemically generated silver nanoparticles (AgNPs) within a chitosan (CS)-modified, high-surface-area activated carbon derived from kenaf (KAC), using a unique self-activation method. The even distribution of AgNPs was visible in the scanning electron microscopy images and a Fourier transform infra red study demonstrated major absorption peaks. The experimental results revealed that KA-CS-AgNPs exhibited exceptional adsorption efficiency for copper (Cu²⁺), lead (Pb²⁺), and Congo Red dye (CR), and showed potent antibacterial activity against Staphylococcus aureus and Escherichia coli. The maximum adsorption capacity (mg g⁻¹) of KAC-CS-AgNPs was 71.5 for Cu²⁺, 72.3 for Pb²⁺, and 75.9 for CR, and the adsorption phenomena followed on the Freundlich and Langmuir isotherm models and the second-order kinetic model (R² > 0.99). KAC-CS-AgNPs also exhibited excellent reusability of up to four consecutive cycles with minor losses in adsorption ability. The thermodynamic parameters indicated that the adsorption process was spontaneous and endothermic in nature. The bacterial inactivation tests demonstrated that KAC-CS-AgNPs had a strong bactericidal effect on both E. coli and S. aureus, with MIC calculated for E. coli and S. aureus as 32 µg mL⁻¹ and 44 µg mL⁻¹, respectively. The synthesized bioinspired nanocomposite KAC-CS-AgNPs could be an innovative solution for effective and sustainable wastewater treatment and has great potential for commercial applications. Full article

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