Biomolecules

15 pages, 1172 KiB

Open AccessReview

Transcriptional Regulation Technology for Gene Perturbation in Fission Yeast

by Ken Ishikawa and Shigeaki Saitoh

Biomolecules 2023, 13(4), 716; https://doi.org/10.3390/biom13040716 - 21 Apr 2023

Viewed by 1604

Isolation and introduction of genetic mutations is the primary approach to characterize gene functions in model yeasts. Although this approach has proven very powerful, it is not applicable to all genes in these organisms. For example, introducing defective mutations into essential genes causes [...] Read more.

Isolation and introduction of genetic mutations is the primary approach to characterize gene functions in model yeasts. Although this approach has proven very powerful, it is not applicable to all genes in these organisms. For example, introducing defective mutations into essential genes causes lethality upon loss of function. To circumvent this difficulty, conditional and partial repression of target transcription is possible. While transcriptional regulation techniques, such as promoter replacement and 3′ untranslated region (3′UTR) disruption, are available for yeast systems, CRISPR–Cas-based technologies have provided additional options. This review summarizes these gene perturbation technologies, including recent advances in methods based on CRISPR–Cas systems for Schizosaccharomyces pombe. We discuss how biological resources afforded by CRISPRi can promote fission yeast genetics. Full article

(This article belongs to the Special Issue Yeast Models for Gene Regulation)

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15 pages, 1638 KiB

Open AccessEditor’s ChoiceArticle

Adenosine A_2A Receptors Shut Down Adenosine A₁ Receptor-Mediated Presynaptic Inhibition to Promote Implementation of Hippocampal Long-Term Potentiation

by Cátia R. Lopes, Francisco Q. Gonçalves, Simão Olaio, Angelo R. Tomé, Rodrigo A. Cunha and João Pedro Lopes

Biomolecules 2023, 13(4), 715; https://doi.org/10.3390/biom13040715 - 21 Apr 2023

Cited by 5 | Viewed by 1490

Abstract

Adenosine operates a modulation system fine-tuning the efficiency of synaptic transmission and plasticity through A₁ and A_2A receptors (A₁R, A_2AR), respectively. Supramaximal activation of A₁R can block hippocampal synaptic transmission, and the tonic engagement of [...] Read more.

Adenosine operates a modulation system fine-tuning the efficiency of synaptic transmission and plasticity through A₁ and A_2A receptors (A₁R, A_2AR), respectively. Supramaximal activation of A₁R can block hippocampal synaptic transmission, and the tonic engagement of A₁R-mediated inhibition is increased with increased frequency of nerve stimulation. This is compatible with an activity-dependent increase in extracellular adenosine in hippocampal excitatory synapses, which can reach levels sufficient to block synaptic transmission. We now report that A_2AR activation decreases A₁R-medated inhibition of synaptic transmission, with particular relevance during high-frequency-induced long-term potentiation (LTP). Thus, whereas the A₁R antagonist DPCPX (50 nM) was devoid of effects on LTP magnitude, the addition of an A_2AR antagonist SCH58261 (50 nM) allowed a facilitatory effect of DPCPX on LTP to be revealed. Additionally, the activation of A_2AR with CGS21680 (30 nM) decreased the potency of the A₁R agonist CPA (6–60 nM) to inhibit hippocampal synaptic transmission in a manner prevented by SCH58261. These observations show that A_2AR play a key role in dampening A₁R during high-frequency induction of hippocampal LTP. This provides a new framework for understanding how the powerful adenosine A₁R-mediated inhibition of excitatory transmission can be controlled to allow the implementation of hippocampal LTP. Full article

(This article belongs to the Special Issue Pharmacology of Purinergic Receptors—Honorary Special Issue Dedicated to Prof. Pier Andrea Borea)

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20 pages, 21947 KiB

Open AccessArticle

Transcriptome Analysis of Redox Systems and Polyamine Metabolic Pathway in Hepatoma and Non-Tumor Hepatocyte-like Cells

by Olga N. Ivanova, George S. Krasnov, Anastasiya V. Snezhkina, Anna V. Kudryavtseva, Vyacheslav S. Fedorov, Natalia F. Zakirova, Michail V. Golikov, Sergey N. Kochetkov, Birke Bartosch, Vladimir T. Valuev-Elliston and Alexander V. Ivanov

Biomolecules 2023, 13(4), 714; https://doi.org/10.3390/biom13040714 - 21 Apr 2023

Cited by 1 | Viewed by 1953

Abstract

Reactive oxygen species (ROS) play a major role in the regulation of various processes in the cell. The increase in their production is a factor contributing to the development of numerous pathologies, including inflammation, fibrosis, and cancer. Accordingly, the study of ROS production [...] Read more.

Reactive oxygen species (ROS) play a major role in the regulation of various processes in the cell. The increase in their production is a factor contributing to the development of numerous pathologies, including inflammation, fibrosis, and cancer. Accordingly, the study of ROS production and neutralization, as well as redox-dependent processes and the post-translational modifications of proteins, is warranted. Here, we present a transcriptomic analysis of the gene expression of various redox systems and related metabolic processes, such as polyamine and proline metabolism and the urea cycle in Huh7.5 hepatoma cells and the HepaRG liver progenitor cell line, that are widely used in hepatitis research. In addition, changes in response to the activation of polyamine catabolism that contribute to oxidative stress were studied. In particular, differences in the gene expression of various ROS-producing and ROS-neutralizing proteins, the enzymes of polyamine metabolisms and proline and urea cycles, as well as calcium ion transporters between cell lines, are shown. The data obtained are important for understanding the redox biology of viral hepatitis and elucidating the influence of the laboratory models used. Full article

(This article belongs to the Special Issue Polyamine Metabolism and Function)

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14 pages, 5857 KiB

Open AccessArticle

Downregulation of Bmal1 Expression in Celiac Ganglia Protects against Hepatic Ischemia-Reperfusion Injury

by Jiarui Feng, Lilong Zhang, Enfu Xue, Zhendong Qiu, Ning Hu, Kunpeng Wang, Yingru Su and Weixing Wang

Biomolecules 2023, 13(4), 713; https://doi.org/10.3390/biom13040713 - 21 Apr 2023

Viewed by 1449

Abstract

Hepatic ischemia-reperfusion injury (HIRI) significantly contributes to liver dysfunction following liver transplantation and hepatectomy. However, the role of the celiac ganglion (CG) in HIRI remains unclear. Adeno-associated virus was used to silence Bmal1 expression in the CG of twelve beagles that were randomly [...] Read more.

Hepatic ischemia-reperfusion injury (HIRI) significantly contributes to liver dysfunction following liver transplantation and hepatectomy. However, the role of the celiac ganglion (CG) in HIRI remains unclear. Adeno-associated virus was used to silence Bmal1 expression in the CG of twelve beagles that were randomly assigned to the Bmal1 knockdown group (KO-Bmal1) and the control group. After four weeks, a canine HIRI model was established, and CG, liver tissue, and serum samples were collected for analysis. The virus significantly downregulated Bmal1 expression in the CG. Immunofluorescence staining confirmed a lower proportion of c-fos⁺ and NGF⁺ neurons in TH⁺ cells in the KO-Bmal1 group than in the control group. The KO-Bmal1 group exhibited lower Suzuki scores and serum ALT and AST levels than the control group. Bmal1 knockdown significantly reduced liver fat reserve, hepatocyte apoptosis, and liver fibrosis, and it increased liver glycogen accumulation. We also observed that Bmal1 downregulation inhibited the hepatic neurotransmitter norepinephrine, neuropeptide Y levels, and sympathetic nerve activity in HIRI. Finally, we confirmed that decreased Bmal1 expression in CG reduces TNF-α, IL-1β, and MDA levels and increases GSH levels in the liver. The downregulation of Bmal1 expression in CG suppresses neural activity and improves hepatocyte injury in the beagle model after HIRI. Full article

(This article belongs to the Special Issue The Advanced Research on Animal Nutrition and by-Product Treatment)

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18 pages, 3567 KiB

Open AccessReview

Mechanisms of Diseases Associated with Mutation in GJC2/Connexin 47

by Charles K. Abrams

Biomolecules 2023, 13(4), 712; https://doi.org/10.3390/biom13040712 - 21 Apr 2023

Cited by 3 | Viewed by 1621

Abstract

Connexins are members of a family of integral membrane proteins that provide a pathway for both electrical and metabolic coupling between cells. Astroglia express connexin 30 (Cx30)-GJB6 and Cx43-GJA1, while oligodendroglia express Cx29/Cx31.3-GJC3, Cx32-GJB1, and Cx47- [...] Read more.

Connexins are members of a family of integral membrane proteins that provide a pathway for both electrical and metabolic coupling between cells. Astroglia express connexin 30 (Cx30)-GJB6 and Cx43-GJA1, while oligodendroglia express Cx29/Cx31.3-GJC3, Cx32-GJB1, and Cx47-GJC2. Connexins organize into hexameric hemichannels (homomeric if all subunits are identical or heteromeric if one or more differs). Hemichannels from one cell then form cell-cell channels with a hemichannel from an apposed cell. (These are termed homotypic if the hemichannels are identical and heterotypic if the hemichannels differ). Oligodendrocytes couple to each other through Cx32/Cx32 or Cx47/Cx47 homotypic channels and they couple to astrocytes via Cx32/Cx30 or Cx47/Cx43 heterotypic channels. Astrocytes couple via Cx30/Cx30 and Cx43/Cx43 homotypic channels. Though Cx32 and Cx47 may be expressed in the same cells, all available data suggest that Cx32 and Cx47 cannot interact heteromerically. Animal models wherein one or in some cases two different CNS glial connexins have been deleted have helped to clarify the role of these molecules in CNS function. Mutations in a number of different CNS glial connexin genes cause human disease. Mutations in GJC2 lead to three distinct phenotypes, Pelizaeus Merzbacher like disease, hereditary spastic paraparesis (SPG44) and subclinical leukodystrophy. Full article

(This article belongs to the Special Issue Role of Connexins in Hereditary Diseases)

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21 pages, 4159 KiB

Open AccessEditor’s ChoiceArticle

A Soluble Platelet-Derived Growth Factor Receptor-β Originates via Pre-mRNA Splicing in the Healthy Brain and Is Upregulated during Hypoxia and Aging

by Laura Beth Payne, Hanaa Abdelazim, Maruf Hoque, Audra Barnes, Zuzana Mironovova, Caroline E. Willi, Jordan Darden, Clifton Houk, Meghan W. Sedovy, Scott R. Johnstone and John C. Chappell

Biomolecules 2023, 13(4), 711; https://doi.org/10.3390/biom13040711 - 21 Apr 2023

Cited by 1 | Viewed by 2374

Abstract

The platelet-derived growth factor-BB (PDGF-BB) pathway provides critical regulation of cerebrovascular pericytes, orchestrating their investment and retention within the brain microcirculation. Dysregulated PDGF Receptor-beta (PDGFRβ) signaling can lead to pericyte defects that compromise blood-brain barrier (BBB) integrity and cerebral perfusion, impairing neuronal activity [...] Read more.

The platelet-derived growth factor-BB (PDGF-BB) pathway provides critical regulation of cerebrovascular pericytes, orchestrating their investment and retention within the brain microcirculation. Dysregulated PDGF Receptor-beta (PDGFRβ) signaling can lead to pericyte defects that compromise blood-brain barrier (BBB) integrity and cerebral perfusion, impairing neuronal activity and viability, which fuels cognitive and memory deficits. Receptor tyrosine kinases such as PDGF-BB and vascular endothelial growth factor-A (VEGF-A) are often modulated by soluble isoforms of cognate receptors that establish signaling activity within a physiological range. Soluble PDGFRβ (sPDGFRβ) isoforms have been reported to form by enzymatic cleavage from cerebrovascular mural cells, and pericytes in particular, largely under pathological conditions. However, pre-mRNA alternative splicing has not been widely explored as a possible mechanism for generating sPDGFRβ variants, and specifically during tissue homeostasis. Here, we found sPDGFRβ protein in the murine brain and other tissues under normal, physiological conditions. Utilizing brain samples for follow-on analysis, we identified mRNA sequences corresponding to sPDGFRβ isoforms, which facilitated construction of predicted protein structures and related amino acid sequences. Human cell lines yielded comparable sequences and protein model predictions. Retention of ligand binding capacity was confirmed for sPDGFRβ by co-immunoprecipitation. Visualizing fluorescently labeled sPDGFRβ transcripts revealed a spatial distribution corresponding to murine brain pericytes alongside cerebrovascular endothelium. Soluble PDGFRβ protein was detected throughout the brain parenchyma in distinct regions, such as along the lateral ventricles, with signals also found more broadly adjacent to cerebral microvessels consistent with pericyte labeling. To better understand how sPDGFRβ variants might be regulated, we found elevated transcript and protein levels in the murine brain with age, and acute hypoxia increased sPDGFRβ variant transcripts in a cell-based model of intact vessels. Our findings indicate that soluble isoforms of PDGFRβ likely arise from pre-mRNA alternative splicing, in addition to enzymatic cleavage mechanisms, and these variants exist under normal physiological conditions. Follow-on studies will be needed to establish potential roles for sPDGFRβ in regulating PDGF-BB signaling to maintain pericyte quiescence, BBB integrity, and cerebral perfusion—critical processes underlying neuronal health and function, and in turn, memory and cognition. Full article

(This article belongs to the Special Issue The Role of Vascular Dysfunction in Neuronal Degeneration and Cognitive Impairment)

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16 pages, 4415 KiB

Open AccessReview

Small Molecules Targeting Kidney ClC-K Chloride Channels: Applications in Rare Tubulopathies and Common Cardiovascular Diseases

by Maria Antonietta Coppola, Michael Pusch, Paola Imbrici and Antonella Liantonio

Biomolecules 2023, 13(4), 710; https://doi.org/10.3390/biom13040710 - 21 Apr 2023

Cited by 1 | Viewed by 1912

Abstract

Given the key role played by ClC-K chloride channels in kidney and inner ear physiology and pathology, they can be considered important targets for drug discovery. Indeed, ClC-Ka and ClC-Kb inhibition would interfere with the urine countercurrent concentration mechanism in Henle’s loop, which [...] Read more.

Given the key role played by ClC-K chloride channels in kidney and inner ear physiology and pathology, they can be considered important targets for drug discovery. Indeed, ClC-Ka and ClC-Kb inhibition would interfere with the urine countercurrent concentration mechanism in Henle’s loop, which is responsible for the reabsorption of water and electrolytes from the collecting duct, producing a diuretic and antihypertensive effect. On the other hand, ClC-K/barttin channel dysfunctions in Bartter Syndrome with or without deafness will require the pharmacological recovery of channel expression and/or activity. In these cases, a channel activator or chaperone would be appealing. Starting from a brief description of the physio-pathological role of ClC-K channels in renal function, this review aims to provide an overview of the recent progress in the discovery of ClC-K channel modulators. Full article

(This article belongs to the Special Issue Defects in the Transport Mechanism of Membrane Proteins and Related Diseases)

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20 pages, 847 KiB

Open AccessEditor’s ChoiceReview

Vitamin D and Autoimmune Rheumatic Diseases

by Lambros Athanassiou, Ifigenia Kostoglou-Athanassiou, Michael Koutsilieris and Yehuda Shoenfeld

Biomolecules 2023, 13(4), 709; https://doi.org/10.3390/biom13040709 - 21 Apr 2023

Cited by 12 | Viewed by 5745

Abstract

Vitamin D is a steroid hormone with potent immune-modulating properties. It has been shown to stimulate innate immunity and induce immune tolerance. Extensive research efforts have shown that vitamin D deficiency may be related to the development of autoimmune diseases. Vitamin D deficiency [...] Read more.

Vitamin D is a steroid hormone with potent immune-modulating properties. It has been shown to stimulate innate immunity and induce immune tolerance. Extensive research efforts have shown that vitamin D deficiency may be related to the development of autoimmune diseases. Vitamin D deficiency has been observed in patients with rheumatoid arthritis (RA) and has been shown to be inversely related to disease activity. Moreover, vitamin D deficiency may be implicated in the pathogenesis of the disease. Vitamin D deficiency has also been observed in patients with systemic lupus erythematosus (SLE). It has been found to be inversely related to disease activity and renal involvement. In addition, vitamin D receptor polymorphisms have been studied in SLE. Vitamin D levels have been studied in patients with Sjogren’s syndrome, and vitamin D deficiency may be related to neuropathy and the development of lymphoma in the context of Sjogren’s syndrome. Vitamin D deficiency has been observed in ankylosing spondylitis, psoriatic arthritis (PsA), and idiopathic inflammatory myopathies. Vitamin D deficiency has also been observed in systemic sclerosis. Vitamin D deficiency may be implicated in the pathogenesis of autoimmunity, and it may be administered to prevent autoimmune disease and reduce pain in the context of autoimmune rheumatic disorders. Full article

(This article belongs to the Section Molecular Medicine)

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14 pages, 2651 KiB

Open AccessArticle

Skeletal Muscle Atrophy Induced by Diabetes Is Mediated by Non-Selective Channels and Prevented by Boldine

by Luis A. Cea, Walter Vásquez, Romina Hernández-Salinas, Alejandra Z. Vielma, Mario Castillo-Ruiz, Victoria Velarde, Magdiel Salgado and Juan C. Sáez

Biomolecules 2023, 13(4), 708; https://doi.org/10.3390/biom13040708 - 21 Apr 2023

Cited by 4 | Viewed by 1732

Abstract

Individuals with diabetes mellitus present a skeletal muscle myopathy characterized by atrophy. However, the mechanism underlying this muscular alteration remains elusive, which makes it difficult to design a rational treatment that could avoid the negative consequences in muscles due to diabetes. In the [...] Read more.

Individuals with diabetes mellitus present a skeletal muscle myopathy characterized by atrophy. However, the mechanism underlying this muscular alteration remains elusive, which makes it difficult to design a rational treatment that could avoid the negative consequences in muscles due to diabetes. In the present work, the atrophy of skeletal myofibers from streptozotocin-induced diabetic rats was prevented with boldine, suggesting that non-selective channels inhibited by this alkaloid are involved in this process, as has previously shown for other muscular pathologies. Accordingly, we found a relevant increase in sarcolemma permeability of skeletal myofibers of diabetic animals in vivo and in vitro due to de novo expression of functional connexin hemichannels (Cx HCs) containing connexins (Cxs) 39, 43, and 45. These cells also expressed P2X₇ receptors, and their inhibition in vitro drastically reduced sarcolemma permeability, suggesting their participation in the activation of Cx HCs. Notably, sarcolemma permeability of skeletal myofibers was prevented by boldine treatment that blocks Cx43 and Cx45 HCs, and now we demonstrated that it also blocks P2X₇ receptors. In addition, the skeletal muscle alterations described above were not observed in diabetic mice with myofibers deficient in Cx43/Cx45 expression. Moreover, murine myofibers cultured for 24 h in high glucose presented a drastic increase in sarcolemma permeability and levels of NLRP3, a molecular member of the inflammasome, a response that was also prevented by boldine, suggesting that, in addition to the systemic inflammatory response found in diabetes, high glucose can promote the expression of functional Cx HCs and activation of the inflammasome in skeletal myofibers. Therefore, Cx43 and Cx45 HCs play a critical role in myofiber degeneration, and boldine could be considered a potential therapeutic agent to treat muscular complications due to diabetes. Full article

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

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19 pages, 3404 KiB

Open AccessFeature PaperArticle

Dose-Dependent Effects in Plasma Oncotherapy: Critical In Vivo Immune Responses Missed by In Vitro Studies

by Yuanyuan He, Fanwu Gong, Tao Jin, Qi Liu, Haopeng Fang, Yan Chen, Guomin Wang, Paul K. Chu, Zhengwei Wu and Kostya (Ken) Ostrikov

Biomolecules 2023, 13(4), 707; https://doi.org/10.3390/biom13040707 - 21 Apr 2023

Cited by 4 | Viewed by 2141

Abstract

Cold atmospheric plasma (CAP) generates abundant reactive oxygen and nitrogen species (ROS and RNS, respectively) which can induce apoptosis, necrosis, and other biological responses in tumor cells. However, the frequently observed different biological responses to in vitro and in vivo CAP treatments remain [...] Read more.

Cold atmospheric plasma (CAP) generates abundant reactive oxygen and nitrogen species (ROS and RNS, respectively) which can induce apoptosis, necrosis, and other biological responses in tumor cells. However, the frequently observed different biological responses to in vitro and in vivo CAP treatments remain poorly understood. Here, we reveal and explain plasma-generated ROS/RNS doses and immune system-related responses in a focused case study of the interactions of CAP with colon cancer cells in vitro and with the corresponding tumor in vivo. Plasma controls the biological activities of MC38 murine colon cancer cells and the involved tumor-infiltrating lymphocytes (TILs). In vitro CAP treatment causes necrosis and apoptosis in MC38 cells, which is dependent on the generated doses of intracellular and extracellular ROS/RNS. However, in vivo CAP treatment for 14 days decreases the proportion and number of tumor-infiltrating CD8⁺T cells while increasing PD-L1 and PD-1 expression in the tumors and the TILs, which promotes tumor growth in the studied C57BL/6 mice. Furthermore, the ROS/RNS levels in the tumor interstitial fluid of the CAP-treated mice are significantly lower than those in the MC38 cell culture supernatant. The results indicate that low doses of ROS/RNS derived from in vivo CAP treatment may activate the PD-1/PD-L1 signaling pathway in the tumor microenvironment and lead to the undesired tumor immune escape. Collectively, these results suggest the crucial role of the effect of doses of plasma-generated ROS and RNS, which are generally different in in vitro and in vivo treatments, and also suggest that appropriate dose adjustments are required upon translation to real-world plasma oncotherapy. Full article

(This article belongs to the Special Issue Advances in Plasma Bioscience and Medicine)

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10 pages, 1059 KiB

Open AccessArticle

Deregulation of Plasma microRNA Expression in a TARDBP-ALS Family

by Paola Ruffo, Stefania Catalano, Vincenzo La Bella and Francesca Luisa Conforti

Biomolecules 2023, 13(4), 706; https://doi.org/10.3390/biom13040706 - 21 Apr 2023

Cited by 3 | Viewed by 1329

Abstract

TDP-43 intracellular aggregates are a pathogenic sign of most amyotrophic lateral sclerosis (ALS) cases. Familial ALS, brought on by TARDBP gene mutations, emphasizes the relevance of this altered protein in pathophysiology. Growing evidence suggests a role for dysregulated microRNA (miRNA) in ALS disease. [...] Read more.

TDP-43 intracellular aggregates are a pathogenic sign of most amyotrophic lateral sclerosis (ALS) cases. Familial ALS, brought on by TARDBP gene mutations, emphasizes the relevance of this altered protein in pathophysiology. Growing evidence suggests a role for dysregulated microRNA (miRNA) in ALS disease. Furthermore, several studies showed that miRNAs are highly stable in various biological fluids (CSF, blood, plasma, and serum), and they are expressed differentially by comparing ALS patients and controls. In 2011, our research group discovered a rare mutation in a TARDBP gene (G376D) in a large ALS Apulian family with affected members exhibiting a rapidly progressing disease. To identify potential non-invasive biomarkers of preclinical and clinical progression in the TARDBP-ALS family, we assessed the expression levels of plasma microRNAs in affected patients (n = 7) and asymptomatic mutation carriers (n = 7) compared with healthy controls (n = 13). Applying qPCR, we investigate 10 miRNAs that bind TDP-43 in vitro during their biogenesis or in their mature form, and the other nine are known to be deregulated in the disease. We highlight the potential of miR-132-5p, miR-132-3p, miR-124-3p, and miR-133a-3p expression levels in plasma as biomarkers of preclinical progression for G376D-TARDBP-associated ALS. Our research strongly supports the potential of plasma miRNAs as biomarkers for performing predictive diagnostics and identifying new therapeutic targets. Full article

(This article belongs to the Special Issue Molecular Basis of Neuromuscular Diseases 2.0)

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1 pages, 161 KiB

Open AccessCorrection

Correction: Tian et al. The Underlying Role of the Glymphatic System and Meningeal Lymphatic Vessels in Cerebral Small Vessel Disease. Biomolecules 2022, 12, 748

by Yu Tian, Mengxi Zhao, Yiyi Chen, Mo Yang and Yilong Wang

Biomolecules 2023, 13(4), 705; https://doi.org/10.3390/biom13040705 - 21 Apr 2023

Cited by 2 | Viewed by 712

Abstract

In the published publication [...] Full article

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

13 pages, 2495 KiB

Open AccessArticle

Electronic Circular Dichroism Detects Conformational Changes Associated with Proteasome Gating Confirmed Using AFM Imaging

by Alessandro D’Urso, Roberto Purrello, Alessandra Cunsolo, Danilo Milardi, Caterina Fattorusso, Marco Persico, Maria Gaczynska, Pawel A. Osmulski and Anna Maria Santoro

Biomolecules 2023, 13(4), 704; https://doi.org/10.3390/biom13040704 - 20 Apr 2023

Viewed by 1348

Abstract

Many chronic diseases, including cancer and neurodegeneration, are linked to proteasome dysregulation. Proteasome activity, essential for maintaining proteostasis in a cell, is controlled by the gating mechanism and its underlying conformational transitions. Thus, developing effective methods to detect gate-related specific proteasome conformations could [...] Read more.

Many chronic diseases, including cancer and neurodegeneration, are linked to proteasome dysregulation. Proteasome activity, essential for maintaining proteostasis in a cell, is controlled by the gating mechanism and its underlying conformational transitions. Thus, developing effective methods to detect gate-related specific proteasome conformations could be a significant contribution to rational drug design. Since the structural analysis suggests that gate opening is associated with a decrease in the content of α-helices and β-sheets and an increase in random coil structures, we decided to explore the application of electronic circular dichroism (ECD) in the UV region to monitor the proteasome gating. A comparison of ECD spectra of wild type yeast 20S proteasome (predominantly closed) and an open-gate mutant (α3ΔN) revealed an increased intensity in the ECD band at 220 nm, which suggests increased contents of random coil and β-turn structures. This observation was further supported by evaluating ECD spectra of human 20S treated with low concentration of SDS, known as a gate-opening reagent. Next, to evaluate the power of ECD to probe a ligand-induced gate status, we treated the proteasome with H2T4, a tetracationic porphyrin that we showed previously to induce large-scale protein conformational changes upon binding to h20S. H2T4 caused a significant increase in the ECD band at 220 nm, interpreted as an induced opening of the 20S gate. In parallel, we imaged the gate-harboring alpha ring of the 20S with AFM, a technique that we used previously to visualize the predominantly closed gate in latent human or yeast 20S and the open gate in α3ΔN mutant. The results were convergent with the ECD data and showed a marked decrease in the content of closed-gate conformation in the H2T4-treated h20S. Our findings provide compelling support for the use of ECD measurements to conveniently monitor proteasome conformational changes related to gating phenomena. We predict that the observed association of spectroscopic and structural results will help with efficient design and characterization of exogenous proteasome regulators. Full article

(This article belongs to the Special Issue Hemoproteins and Proteolytic Enzymes: Variations on the Theme of Functional Modulation: A Themed Issue in Honor of Professor Massimo Coletta)

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12 pages, 285 KiB

Open AccessReview

Classification and Antigen Molecules of Autoimmune Bullous Diseases

by Takashi Hashimoto, Hua Qian, Norito Ishii, Takekuni Nakama, Chiharu Tateishi, Daisuke Tsuruta and Xiaoguang Li

Biomolecules 2023, 13(4), 703; https://doi.org/10.3390/biom13040703 - 20 Apr 2023

Cited by 1 | Viewed by 1466

Abstract

Autoimmune bullous diseases (AIBDs), which are a group of tissue-specific autoimmune diseases of the skin, present with various blistering lesions on the skin and mucous membranes, and show autoantibodies of IgG, IgA and IgM against epidermal cell surfaces and basement membrane zone. To [...] Read more.

Autoimmune bullous diseases (AIBDs), which are a group of tissue-specific autoimmune diseases of the skin, present with various blistering lesions on the skin and mucous membranes, and show autoantibodies of IgG, IgA and IgM against epidermal cell surfaces and basement membrane zone. To date, AIBDs have been classified into a number of distinct subtypes by clinical and histopathological findings, and immunological characteristics. In addition, various biochemical and molecular biological studies have identified various novel autoantigens in AIBDs, which has resulted in proposals of new subtypes of AIBDs. In this article, we summarized various distinct AIBDs, and proposed the latest and most comprehensive classification of AIBDs with their autoantigen molecules. Full article

(This article belongs to the Special Issue Pathogenesis and Drug Development for Non-communicable Inflammatory Skin Diseases)

17 pages, 1152 KiB

Open AccessReview

VEGFA Isoforms as Pro-Angiogenic Therapeutics for Cerebrovascular Diseases

by Amanda Louise White and Gregory Jaye Bix

Biomolecules 2023, 13(4), 702; https://doi.org/10.3390/biom13040702 - 20 Apr 2023

Cited by 5 | Viewed by 1395

Abstract

Therapeutic angiogenesis has long been considered a viable treatment for vasculature disruptions, including cerebral vasculature diseases. One widely-discussed treatment method to increase angiogenesis is vascular endothelial growth factor (VEGF) A. In animal models, treatment with VEGFA proved beneficial, resulting in increased angiogenesis, increased [...] Read more.

Therapeutic angiogenesis has long been considered a viable treatment for vasculature disruptions, including cerebral vasculature diseases. One widely-discussed treatment method to increase angiogenesis is vascular endothelial growth factor (VEGF) A. In animal models, treatment with VEGFA proved beneficial, resulting in increased angiogenesis, increased neuronal density, and improved outcome. However, VEGFA administration in clinical trials has thus far failed to replicate the promising results seen in animal models. The lack of beneficial effects in humans and the difficulty in medicinal translation may be due in part to administration methods and VEGFA’s ability to increase vascular permeability. One solution to mitigate the side effects of VEGFA may be found in the VEGFA isoforms. VEGFA is able to produce several different isoforms through alternative splicing. Each VEGFA isoform interacts differently with both the cellular components and the VEGF receptors. Because of the different biological effects elicited, VEGFA isoforms may hold promise as a tangible potential therapeutic for cerebrovascular diseases. Full article

(This article belongs to the Special Issue Neurotrophic Factors and Growth Factors - Historical Perspective and New Directions for Medical Use)

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13 pages, 8029 KiB

Open AccessArticle

Functional Proteomic Profiling Analysis in Four Major Types of Gastrointestinal Cancers

by Yangyang Wang, Xiaoguang Gao and Jihan Wang

Biomolecules 2023, 13(4), 701; https://doi.org/10.3390/biom13040701 - 20 Apr 2023

Cited by 1 | Viewed by 1306

Abstract

Gastrointestinal (GI) cancer accounts for one in four cancer cases and one in three cancer-related deaths globally. A deeper understanding of cancer development mechanisms can be applied to cancer medicine. Comprehensive sequencing applications have revealed the genomic landscapes of the common types of [...] Read more.

Gastrointestinal (GI) cancer accounts for one in four cancer cases and one in three cancer-related deaths globally. A deeper understanding of cancer development mechanisms can be applied to cancer medicine. Comprehensive sequencing applications have revealed the genomic landscapes of the common types of human cancer, and proteomics technology has identified protein targets and signalling pathways related to cancer growth and progression. This study aimed to explore the functional proteomic profiles of four major types of GI tract cancer based on The Cancer Proteome Atlas (TCPA). We provided an overview of functional proteomic heterogeneity by performing several approaches, including principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), t-stochastic neighbour embedding (t-SNE) analysis, and hierarchical clustering analysis in oesophageal carcinoma (ESCA), stomach adenocarcinoma (STAD), colon adenocarcinoma (COAD), and rectum adenocarcinoma (READ) tumours, to gain a system-wide understanding of the four types of GI cancer. The feature selection approach, mutual information feature selection (MIFS) method, was conducted to screen candidate protein signature subsets to better distinguish different cancer types. The potential clinical implications of candidate proteins in terms of tumour progression and prognosis were also evaluated based on TCPA and The Cancer Genome Atlas (TCGA) databases. The results suggested that functional proteomic profiling can identify different patterns among the four types of GI cancers and provide candidate proteins for clinical diagnosis and prognosis evaluation. We also highlighted the application of feature selection approaches in high-dimensional biological data analysis. Overall, this study could improve the understanding of the complexity of cancer phenotypes and genotypes and thus be applied to cancer medicine. Full article

(This article belongs to the Special Issue Genetics and Genomics of Gastrointestinal Cancers)

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20 pages, 3079 KiB

Open AccessEditor’s ChoiceReview

Protective Effect of Olive Oil Microconstituents in Atherosclerosis: Emphasis on PAF Implicated Atherosclerosis Theory

by Smaragdi Antonopoulou and Constantinos A. Demopoulos

Biomolecules 2023, 13(4), 700; https://doi.org/10.3390/biom13040700 - 20 Apr 2023

Cited by 11 | Viewed by 1665

Abstract

Atherosclerosis is a progressive vascular multifactorial process. The mechanisms underlining the initiating event of atheromatous plaque formation are inflammation and oxidation. Among the modifiable risk factors for cardiovascular diseases, diet and especially the Mediterranean diet (MedDiet), has been widely recognized as one of [...] Read more.

Atherosclerosis is a progressive vascular multifactorial process. The mechanisms underlining the initiating event of atheromatous plaque formation are inflammation and oxidation. Among the modifiable risk factors for cardiovascular diseases, diet and especially the Mediterranean diet (MedDiet), has been widely recognized as one of the healthiest dietary patterns. Olive oil (OO), the main source of the fatty components of the MedDiet is superior to the other “Mono-unsaturated fatty acids containing oils” due to the existence of specific microconstituents. In this review, the effects of OO microconstituents in atherosclerosis, based on data from in vitro and in vivo studies with special attention on their inhibitory activity against PAF (Platelet-Activating Factor) actions, are presented and critically discussed. In conclusion, we propose that the anti-atherogenic effect of OO is attributed to the synergistic action of its microconstituents, mainly polar lipids that act as PAF inhibitors, specific polyphenols and α-tocopherol that also exert anti-PAF activity. This beneficial effect, also mediated through anti-PAF action, can occur from microconstituents extracted from olive pomace, a toxic by-product of the OO production process that constitutes a significant ecological problem. Daily intake of moderate amounts of OO consumed in the context of a balanced diet is significant for healthy adults. Full article

(This article belongs to the Section Cellular Biochemistry)

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25 pages, 6153 KiB

Open AccessFeature PaperArticle

Biomolecules of Fermented Tropical Fruits and Fermenting Microbes as Regulators of Human Hair Loss, Hair Quality, and Scalp Microbiota

by Wolfgang Mayer, Michaela Weibel, Chiara De Luca, Galina Ibragimova, Ilya Trakhtman, Zaira Kharaeva, Danny L. Chandler and Liudmila Korkina

Biomolecules 2023, 13(4), 699; https://doi.org/10.3390/biom13040699 - 20 Apr 2023

Cited by 2 | Viewed by 3128

Abstract

Plant-derived secondary metabolites (polyphenols/terpenes/alkaloids) and microbial exometabolites/membrane components of fermented tropical fruits are known as highly bioavailable biomolecules causing skin and hair improvement effects (wound healing, anti-inflammatory, antioxidant, antidiabetic, antiacne, skin/hair microbiota balancing, hair growth-promoting, and hair loss-inhibiting). Caffein is considered as a [...] Read more.

Plant-derived secondary metabolites (polyphenols/terpenes/alkaloids) and microbial exometabolites/membrane components of fermented tropical fruits are known as highly bioavailable biomolecules causing skin and hair improvement effects (wound healing, anti-inflammatory, antioxidant, antidiabetic, antiacne, skin/hair microbiota balancing, hair growth-promoting, and hair loss-inhibiting). Caffein is considered as a hair growth promoter. A randomized placebo- and caffein-controlled clinical trial on the efficacy of fermented papaya (FP) plus fermented mangosteen (FM) towards human hair quality and loss was conducted. Shampoo and lotion hair care products containing FP, FM, and caffein as active agents were developed and applied to 154 subjects of both sexes with clinically confirmed androgenic or diffuse alopecia for 3 months. Their clinical efficacy was assessed subjectively by questionnaires filled in by dermatologists/trichologists, and by the objective trichomicroscopical calculations. Hair and scalp skin quality was determined by microbiota pattern and ATP, SH-groups, protein, and malonyl dialdehyde quantification. Comparative clinical data showed that the experimental hair care cosmetics significantly inhibited hair loss, increased hair density/thickness, and improved hair follicle structure versus placebo and caffein controls. The cosmetics with FP and FM substantially normalized the microbiota pattern and increased ATP content in hair follicle, while inhibiting lipid peroxidation in the scalp skin, and SH-group formation in the hair shaft. Full article

(This article belongs to the Topic Bioactive Compounds with Application Potentials in Nutraceuticals and Nutricosmetics: Focus on Mechanism of Action and Application Science)

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19 pages, 2581 KiB

Open AccessArticle

Mutational Analysis of Anesthetic Binding Sites and Their Effects on GABA_A Receptor Activation and Modulation by Positive Allosteric Modulators of the α7 Nicotinic Receptor

by Spencer R. Pierce, Allison L. Germann, Sophia Q. Xu, Saumith L. Menon, Marcelo O. Ortells, Hugo R. Arias and Gustav Akk

Biomolecules 2023, 13(4), 698; https://doi.org/10.3390/biom13040698 - 20 Apr 2023

Cited by 1 | Viewed by 1085

Abstract

The positive allosteric modulators (PAMs) of the α7 nicotinic receptor N-(5-Cl-2-hydroxyphenyl)-N′-[2-Cl-5-(trifluoromethyl)phenyl]-urea (NS-1738) and (E)-3-(furan-2-yl)-N-(p-tolyl)-acrylamide (PAM-2) potentiate the α1β2γ2L GABA_A receptor through interactions with the classic anesthetic binding sites located at intersubunit interfaces in [...] Read more.

The positive allosteric modulators (PAMs) of the α7 nicotinic receptor N-(5-Cl-2-hydroxyphenyl)-N′-[2-Cl-5-(trifluoromethyl)phenyl]-urea (NS-1738) and (E)-3-(furan-2-yl)-N-(p-tolyl)-acrylamide (PAM-2) potentiate the α1β2γ2L GABA_A receptor through interactions with the classic anesthetic binding sites located at intersubunit interfaces in the transmembrane domain of the receptor. In the present study, we employed mutational analysis to investigate in detail the involvement and contributions made by the individual intersubunit interfaces to receptor modulation by NS-1738 and PAM-2. We show that mutations to each of the anesthetic-binding intersubunit interfaces (β+/α−, α+/β−, and γ+/β−), as well as the orphan α+/γ− interface, modify receptor potentiation by NS-1738 and PAM-2. Furthermore, mutations to any single interface can fully abolish potentiation by the α7-PAMs. The findings are discussed in the context of energetic additivity and interactions between the individual binding sites. Full article

(This article belongs to the Special Issue GABA(A) Receptors: Structure and Function)

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14 pages, 1066 KiB

Open AccessArticle

Do Serum Galectin-9 Levels in Women with Gestational Diabetes and Healthy Ones Differ before or after Delivery? A Pilot Study

by Aleksandra Pełech, Monika Ruszała, Magdalena Niebrzydowska-Tatus, Katarzyna Bień, Żaneta Kimber-Trojnar, Monika Czuba, Małgorzata Świstowska and Bożena Leszczyńska-Gorzelak

Biomolecules 2023, 13(4), 697; https://doi.org/10.3390/biom13040697 - 20 Apr 2023

Viewed by 1301

Abstract

Gestational diabetes mellitus (GDM) is a common metabolic disease that occurs during pregnancy, with the placenta playing an important role in its pathophysiology. Currently, the role of galectin-9 in the development of GDM is unknown. The aim of this study was to compare [...] Read more.

Gestational diabetes mellitus (GDM) is a common metabolic disease that occurs during pregnancy, with the placenta playing an important role in its pathophysiology. Currently, the role of galectin-9 in the development of GDM is unknown. The aim of this study was to compare galectin-9 concentrations in healthy pregnant women and those with GDM. Galectin-9 levels were assessed in serum samples taken both just before and after delivery, as well as in urine samples collected in the postpartum period. Maternal body composition and hydration status were evaluated using the bioelectrical impedance analysis (BIA) method. There were no statistically significant differences in the concentration of galectin-9 in women with GDM compared to healthy pregnant women in their serum samples taken just before delivery, nor in their serum and urine samples collected in the early postpartum period. However, serum galectin-9 concentrations taken before delivery were positively correlated with BMI and parameters related to the amount of adipose tissue assessed in the early postpartum period. Additionally, there was a correlation between serum galectin-9 concentrations taken before and after delivery. Galectin-9 is unlikely to become a diagnostic marker for GDM. However, this subject requires further clinical research in larger groups. Full article

(This article belongs to the Special Issue Placental-Related Disorders of Pregnancy)

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12 pages, 1047 KiB

Open AccessArticle

Collagen Crosslinking for Keratoconus: Cellular Signaling Mechanisms

by Dimitrios Karamichos, Sarah E. Nicholas, Asher Khan and Kamran M. Riaz

Biomolecules 2023, 13(4), 696; https://doi.org/10.3390/biom13040696 - 20 Apr 2023

Viewed by 1371

Abstract

Collagen crosslinking (CXL) is a widely used treatment to halt the progression of keratoconus (KC). Unfortunately, a significant number of patients with progressive KC will not qualify for CXL, including those with corneas thinner than 400 µm. The present study aimed to investigate [...] Read more.

Collagen crosslinking (CXL) is a widely used treatment to halt the progression of keratoconus (KC). Unfortunately, a significant number of patients with progressive KC will not qualify for CXL, including those with corneas thinner than 400 µm. The present study aimed to investigate the molecular effects of CXL using in vitro models, mirroring the normal, as well as thinner corneal stroma seen in KCs. Primary human corneal stromal cells were isolated from healthy (HCFs) and keratoconus (HKCs) donors. Cells were cultured and stimulated with stable Vitamin C resulting in 3D self-assembled extracellular matrix (ECM), cell-embedded, constructs. CXL was performed on (a) thin ECM with CXL performed at week 2 and (b) normal ECM with CXL performed at week 4. Constructs without CXL served as controls. All constructs were processed for protein analysis. The results showed modulation of Wnt signaling, following CXL treatment, as measured by the protein levels of Wnt7b and Wnt10a, correlated to the expression of α-smooth muscle actin (SMA). Further, the expression of a recently identified KC biomarker candidate, prolactin-induced protein (PIP), was positively impacted by CXL in HKCs. CXL-driven upregulation of PGC-1 and the downregulation of SRC and Cyclin D1 in HKCs were also noted. Although the cellular/molecular impacts of CXL are largely understudied, our studies provide an approximation to the complex mechanisms of KC and CXL. Further studies are warranted to determine factors influencing CXL outcomes. Full article

(This article belongs to the Special Issue Ocular Damage and Wound Healing: From Mechanisms Exploration to Treatment)

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16 pages, 364 KiB

Open AccessReview

Connecting Dots between Mitochondrial Dysfunction and Depression

by Mehtab Khan, Yann Baussan and Etienne Hebert-Chatelain

Biomolecules 2023, 13(4), 695; https://doi.org/10.3390/biom13040695 - 20 Apr 2023

Cited by 9 | Viewed by 3924

Abstract

Mitochondria are the prime source of cellular energy, and are also responsible for important processes such as oxidative stress, apoptosis and Ca²⁺ homeostasis. Depression is a psychiatric disease characterized by alteration in the metabolism, neurotransmission and neuroplasticity. In this manuscript, we summarize [...] Read more.

Mitochondria are the prime source of cellular energy, and are also responsible for important processes such as oxidative stress, apoptosis and Ca²⁺ homeostasis. Depression is a psychiatric disease characterized by alteration in the metabolism, neurotransmission and neuroplasticity. In this manuscript, we summarize the recent evidence linking mitochondrial dysfunction to the pathophysiology of depression. Impaired expression of mitochondria-related genes, damage to mitochondrial membrane proteins and lipids, disruption of the electron transport chain, higher oxidative stress, neuroinflammation and apoptosis are all observed in preclinical models of depression and most of these parameters can be altered in the brain of patients with depression. A deeper knowledge of the depression pathophysiology and the identification of phenotypes and biomarkers with respect to mitochondrial dysfunction are needed to help early diagnosis and the development of new treatment strategies for this devastating disorder. Full article

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

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Graphical abstract

18 pages, 4799 KiB

Open AccessArticle

Biological Screening and Crystallographic Studies of Hydroxy γ-Lactone Derivatives to Investigate PPARγ Phosphorylation Inhibition

by Davide Capelli, Giulia Cazzaniga, Matteo Mori, Antonio Laghezza, Fulvio Loiodice, Martina Quaglia, Elisa Negro, Fiorella Meneghetti, Stefania Villa and Roberta Montanari

Biomolecules 2023, 13(4), 694; https://doi.org/10.3390/biom13040694 - 19 Apr 2023

Cited by 1 | Viewed by 1254

Abstract

PPARγ represents a key target for the treatment of type 2 diabetes and metabolic syndrome. To avoid serious adverse effects related to the PPARγ agonism profile of traditional antidiabetic drugs, a new opportunity is represented by the development of molecules acting as inhibitors [...] Read more.

PPARγ represents a key target for the treatment of type 2 diabetes and metabolic syndrome. To avoid serious adverse effects related to the PPARγ agonism profile of traditional antidiabetic drugs, a new opportunity is represented by the development of molecules acting as inhibitors of PPARγ phosphorylation by the cyclin-dependent kinase 5 (CDK5). Their mechanism of action is mediated by the stabilization of the PPARγ β-sheet containing Ser273 (Ser245 in PPARγ isoform 1 nomenclature). In this paper, we report the identification of new γ-hydroxy-lactone-based PPARγ binders from the screening of an in-house library. These compounds exhibit a non-agonist profile towards PPARγ, and one of them prevents Ser245 PPARγ phosphorylation by acting mainly on PPARγ stabilization and exerting a weak CDK5 inhibitory effect. Full article

(This article belongs to the Special Issue PPARs as Key Regulators in Different Diseases)

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33 pages, 7619 KiB

Open AccessEditor’s ChoiceReview

Multiomics Analysis Reveals Novel Genetic Determinants for Lens Differentiation, Structure, and Transparency

by Joshua Disatham, Lisa Brennan, Ales Cvekl and Marc Kantorow

Biomolecules 2023, 13(4), 693; https://doi.org/10.3390/biom13040693 - 19 Apr 2023

Cited by 4 | Viewed by 2154

Abstract

Recent advances in next-generation sequencing and data analysis have provided new gateways for identification of novel genome-wide genetic determinants governing tissue development and disease. These advances have revolutionized our understanding of cellular differentiation, homeostasis, and specialized function in multiple tissues. Bioinformatic and functional [...] Read more.

Recent advances in next-generation sequencing and data analysis have provided new gateways for identification of novel genome-wide genetic determinants governing tissue development and disease. These advances have revolutionized our understanding of cellular differentiation, homeostasis, and specialized function in multiple tissues. Bioinformatic and functional analysis of these genetic determinants and the pathways they regulate have provided a novel basis for the design of functional experiments to answer a wide range of long-sought biological questions. A well-characterized model for the application of these emerging technologies is the development and differentiation of the ocular lens and how individual pathways regulate lens morphogenesis, gene expression, transparency, and refraction. Recent applications of next-generation sequencing analysis on well-characterized chicken and mouse lens differentiation models using a variety of omics techniques including RNA-seq, ATAC-seq, whole-genome bisulfite sequencing (WGBS), chip-seq, and CUT&RUN have revealed a wide range of essential biological pathways and chromatin features governing lens structure and function. Multiomics integration of these data has established new gene functions and cellular processes essential for lens formation, homeostasis, and transparency including the identification of novel transcription control pathways, autophagy remodeling pathways, and signal transduction pathways, among others. This review summarizes recent omics technologies applied to the lens, methods for integrating multiomics data, and how these recent technologies have advanced our understanding ocular biology and function. The approach and analysis are relevant to identifying the features and functional requirements of more complex tissues and disease states. Full article

(This article belongs to the Special Issue The Genomics Era: From Reference Genomes to Pan-Genomic Graphs)

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23 pages, 21053 KiB

Open AccessArticle

Large-Scale Integration of Single-Cell RNA-Seq Data Reveals Astrocyte Diversity and Transcriptomic Modules across Six Central Nervous System Disorders

by Zhenwei Qian, Jinglin Qin, Yiwen Lai, Chen Zhang and Xiannian Zhang

Biomolecules 2023, 13(4), 692; https://doi.org/10.3390/biom13040692 - 19 Apr 2023

Cited by 2 | Viewed by 4962

Abstract

The dysfunction of astrocytes in response to environmental factors contributes to many neurological diseases by impacting neuroinflammation responses, glutamate and ion homeostasis, and cholesterol and sphingolipid metabolism, which calls for comprehensive and high-resolution analysis. However, single-cell transcriptome analyses of astrocytes have been hampered [...] Read more.

The dysfunction of astrocytes in response to environmental factors contributes to many neurological diseases by impacting neuroinflammation responses, glutamate and ion homeostasis, and cholesterol and sphingolipid metabolism, which calls for comprehensive and high-resolution analysis. However, single-cell transcriptome analyses of astrocytes have been hampered by the sparseness of human brain specimens. Here, we demonstrate how large-scale integration of multi-omics data, including single-cell and spatial transcriptomic and proteomic data, overcomes these limitations. We created a single-cell transcriptomic dataset of human brains by integration, consensus annotation, and analyzing 302 publicly available single-cell RNA-sequencing (scRNA-seq) datasets, highlighting the power to resolve previously unidentifiable astrocyte subpopulations. The resulting dataset includes nearly one million cells that span a wide variety of diseases, including Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD), multiple sclerosis (MS), epilepsy (Epi), and chronic traumatic encephalopathy (CTE). We profiled the astrocytes at three levels, subtype compositions, regulatory modules, and cell–cell communications, and comprehensively depicted the heterogeneity of pathological astrocytes. We constructed seven transcriptomic modules that are involved in the onset and progress of disease development, such as the M2 ECM and M4 stress modules. We validated that the M2 ECM module could furnish potential markers for AD early diagnosis at both the transcriptome and protein levels. In order to accomplish a high-resolution, local identification of astrocyte subtypes, we also carried out a spatial transcriptome analysis of mouse brains using the integrated dataset as a reference. We found that astrocyte subtypes are regionally heterogeneous. We identified dynamic cell–cell interactions in different disorders and found that astrocytes participate in key signaling pathways, such as NRG3-ERBB4, in epilepsy. Our work supports the utility of large-scale integration of single-cell transcriptomic data, which offers new insights into underlying multiple CNS disease mechanisms where astrocytes are involved. Full article

(This article belongs to the Special Issue Applications and Advances of Omics and Bioinformatics in the Research of Alzheimer’s Disease and Complex Phenotypes)

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16 pages, 1380 KiB

Open AccessReview

Nuclear Receptor Gene Variants Underlying Disorders/Differences of Sex Development through Abnormal Testicular Development

by Atsushi Hattori and Maki Fukami

Biomolecules 2023, 13(4), 691; https://doi.org/10.3390/biom13040691 - 19 Apr 2023

Cited by 1 | Viewed by 1295

Abstract

Gonadal development is the first step in human reproduction. Aberrant gonadal development during the fetal period is a major cause of disorders/differences of sex development (DSD). To date, pathogenic variants of three nuclear receptor genes (NR5A1, NR0B1, and NR2F2) [...] Read more.

Gonadal development is the first step in human reproduction. Aberrant gonadal development during the fetal period is a major cause of disorders/differences of sex development (DSD). To date, pathogenic variants of three nuclear receptor genes (NR5A1, NR0B1, and NR2F2) have been reported to cause DSD via atypical testicular development. In this review article, we describe the clinical significance of the NR5A1 variants as the cause of DSD and introduce novel findings from recent studies. NR5A1 variants are associated with 46,XY DSD and 46,XX testicular/ovotesticular DSD. Notably, both 46,XX DSD and 46,XY DSD caused by the NR5A1 variants show remarkable phenotypic variability, to which digenic/oligogenic inheritances potentially contribute. Additionally, we discuss the roles of NR0B1 and NR2F2 in the etiology of DSD. NR0B1 acts as an anti-testicular gene. Duplications containing NR0B1 result in 46,XY DSD, whereas deletions encompassing NR0B1 can underlie 46,XX testicular/ovotesticular DSD. NR2F2 has recently been reported as a causative gene for 46,XX testicular/ovotesticular DSD and possibly for 46,XY DSD, although the role of NR2F2 in gonadal development is unclear. The knowledge about these three nuclear receptors provides novel insights into the molecular networks involved in the gonadal development in human fetuses. Full article

(This article belongs to the Special Issue State-of-the-Art Molecular Reproduction in Japan)

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16 pages, 2997 KiB

Open AccessArticle

High-Glucose Media Reduced the Viability and Induced Differential Pro-Inflammatory Cytokines in Human Periodontal Ligament Fibroblasts

by Alaa Aldoss, Rhodanne Lambarte and Fahd Alsalleeh

Biomolecules 2023, 13(4), 690; https://doi.org/10.3390/biom13040690 - 19 Apr 2023

Viewed by 1650

Abstract

Hyperglycemic condition in diabetic patients tends to exacerbate periodontitis severity. Thus, the influence of hyperglycemia on the biological and inflammatory response of periodontal ligament fibroblasts (PDLFs) needs to be elucidated. In this study, PDLFs were seeded in media containing glucose concentrations (5.5, 25, [...] Read more.

Hyperglycemic condition in diabetic patients tends to exacerbate periodontitis severity. Thus, the influence of hyperglycemia on the biological and inflammatory response of periodontal ligament fibroblasts (PDLFs) needs to be elucidated. In this study, PDLFs were seeded in media containing glucose concentrations (5.5, 25, or 50 mM) and stimulated with 1 µg/mL of lipopolysaccharide (LPS). PDLFs’ viability, cytotoxicity, and the migration ability were determined. The mRNA expression of Interleukin (IL)-6, IL-10, and IL-23 (p19/p40), and Toll-like receptor (TLR)-4 were analyzed; at 6 and 24 h, protein expression of IL-6 and IL-10 was also determined. PDLFs grown in 50 mM glucose medium showed lower viability. The 5.5 mM glucose led to the highest percentage of wound closure compared to 25 mM and 50 mM glucose with/without LPS. Additionally, 50 mM glucose with LPS exhibited the least migration ability among all groups. The expression of IL-6 was amplified significantly in LPS-stimulated cells in 50 mM glucose medium. IL-10 was constitutively expressed in different glucose concentrations, and LPS stimulation decreased it. IL-23 p40 was up-regulated after LPS stimulation in 50 mM glucose concentration. TLR-4 was highly expressed after LPS stimulation in all glucose concentrations. Hyperglycemic conditions limit PDLF proliferation and migration, and enhance the expression of certain pro-inflammatory cytokines to induce periodontitis. Full article

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

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18 pages, 2593 KiB

Open AccessFeature PaperReview

Implications of the Organ-Specific Immune Environment for Immune Priming Effect of Radiotherapy in Metastatic Setting

by Julien Pierrard, Geneviève Van Ooteghem and Marc Van den Eynde

Biomolecules 2023, 13(4), 689; https://doi.org/10.3390/biom13040689 - 18 Apr 2023

Cited by 1 | Viewed by 1224

Abstract

With the development of immune checkpoint inhibitors (ICIs), the tumour immune microenvironment (TIME) has been increasingly considered to improve cancer management. The TIME of metastatic lesions is strongly influenced by the underlying immune contexture of the organ in which they are located. The [...] Read more.

With the development of immune checkpoint inhibitors (ICIs), the tumour immune microenvironment (TIME) has been increasingly considered to improve cancer management. The TIME of metastatic lesions is strongly influenced by the underlying immune contexture of the organ in which they are located. The metastatic location itself appears to be an important prognostic factor in predicting outcomes after ICI treatment in cancer patients. Patients with liver metastases are less likely to respond to ICIs than patients with metastases in other organs, likely due to variations in the metastatic TIME. Combining additional treatment modalities is an option to overcome this resistance. Radiotherapy (RT) and ICIs have been investigated together as an option to treat various metastatic cancers. RT can induce a local and systemic immune reaction, which can promote the patient’s response to ICIs. Here, we review the differential impact of the TIME according to metastatic location. We also explore how RT-induced TIME modifications could be modulated to improve outcomes of RT-ICI combinations. Full article

(This article belongs to the Topic Novel Discoveries in Oncology)

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17 pages, 1129 KiB

Open AccessEditor’s ChoiceReview

The Multifaceted Role of Glutathione S-Transferases in Health and Disease

by Aslam M. A. Mazari, Leilei Zhang, Zhi-Wei Ye, Jie Zhang, Kenneth D. Tew and Danyelle M. Townsend

Biomolecules 2023, 13(4), 688; https://doi.org/10.3390/biom13040688 - 18 Apr 2023

Cited by 23 | Viewed by 4957

Abstract

In humans, the cytosolic glutathione S-transferase (GST) family of proteins is encoded by 16 genes presented in seven different classes. GSTs exhibit remarkable structural similarity with some overlapping functionalities. As a primary function, GSTs play a putative role in Phase II metabolism by [...] Read more.

In humans, the cytosolic glutathione S-transferase (GST) family of proteins is encoded by 16 genes presented in seven different classes. GSTs exhibit remarkable structural similarity with some overlapping functionalities. As a primary function, GSTs play a putative role in Phase II metabolism by protecting living cells against a wide variety of toxic molecules by conjugating them with the tripeptide glutathione. This conjugation reaction is extended to forming redox sensitive post-translational modifications on proteins: S-glutathionylation. Apart from these catalytic functions, specific GSTs are involved in the regulation of stress-induced signaling pathways that govern cell proliferation and apoptosis. Recently, studies on the effects of GST genetic polymorphisms on COVID-19 disease development revealed that the individuals with higher numbers of risk-associated genotypes showed higher risk of COVID-19 prevalence and severity. Furthermore, overexpression of GSTs in many tumors is frequently associated with drug resistance phenotypes. These functional properties make these proteins promising targets for therapeutics, and a number of GST inhibitors have progressed in clinical trials for the treatment of cancer and other diseases. Full article

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

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16 pages, 3307 KiB

Open AccessFeature PaperArticle

Vutiglabridin Modulates Paraoxonase 1 and Ameliorates Diet-Induced Obesity in Hyperlipidemic Mice

by Dawoud Sulaiman, Leo Sungwong Choi, Hyeong Min Lee, Jaejin Shin, Dong Hwan Kim, Keun Woo Lee, Pierre Eftekhari, Angélique Quartier, Hyung Soon Park and Srinivasa T. Reddy

Biomolecules 2023, 13(4), 687; https://doi.org/10.3390/biom13040687 - 18 Apr 2023

Cited by 1 | Viewed by 1370

Abstract

Vutiglabridin is a clinical-stage synthetic small molecule that is being developed for the treatment of obesity and its target proteins have not been fully identified. Paraoxonase-1 (PON1) is an HDL-associated plasma enzyme that hydrolyzes diverse substrates including oxidized low-density lipoprotein (LDL). Furthermore, PON1 [...] Read more.

Vutiglabridin is a clinical-stage synthetic small molecule that is being developed for the treatment of obesity and its target proteins have not been fully identified. Paraoxonase-1 (PON1) is an HDL-associated plasma enzyme that hydrolyzes diverse substrates including oxidized low-density lipoprotein (LDL). Furthermore, PON1 harbors anti-inflammatory and antioxidant capacities and has been implicated as a potential therapeutic target for treating various metabolic diseases. In this study, we performed a non-biased target deconvolution of vutiglabridin using Nematic Protein Organisation Technique (NPOT) and identified PON1 as an interacting protein. We examined this interaction in detail and demonstrate that vutiglabridin binds to PON1 with high affinity and protects PON1 against oxidative damage. Vutiglabridin treatment significantly increased plasma PON1 levels and enzyme activity but not PON1 mRNA in wild-type C57BL/6J mice, suggesting that vutiglabridin modulates PON1 post-transcriptionally. We further investigated the effects of vutiglabridin in obese and hyperlipidemic LDLR^−/− mice and found that it significantly increases plasma PON1 levels, while decreasing body weight, total fat mass, and plasma cholesterol levels. Overall, our results demonstrate that PON1 is a direct, interacting target of vutiglabridin, and that the modulation of PON1 by vutiglabridin may provide benefits for the treatment of hyperlipidemia and obesity. Full article

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

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