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Volume 23
Issue 7
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Int. J. Mol. Sci., Volume 23, Issue 7 (April-1 2022) – 656 articles

Cover Story (view full-size image): Calcific aortic valve disease (CAVD) is a progressive inflammatory disorder characterized by valvular interstitial cell (VIC) osteodifferentiation, leading to valve leaflet calcification and impairment movement. Runt-related transcription factor 2 (Runx2), the master transcription factor involved in VIC osteodifferentiation, modulates the expression of other osteogenic molecules. We designed and obtained vascular cell adhesion molecule (VCAM)-1 targeted lipopolyplexes suitable for systemic administration and targeted delivery of shRNA-Runx2 to osteoblast-differentiated VIC. Our results identify these nanocarriers as a new directed vehicle that could be instrumental in developing novel strategies for blocking the progression of CAVD using a targeted nanomedicine approach. View this paper
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12 pages, 1759 KiB  
Article
Released ATP Mediates Spermatozoa Chemotaxis Promoted by Uterus-Derived Factor (UDF) in Ascaris suum
by Qiushi Wang, Ruijun He, Qi Zhang, Jin Shan, Yanmei Zhao and Xia Wang
Int. J. Mol. Sci. 2022, 23(7), 4069; https://doi.org/10.3390/ijms23074069 - 6 Apr 2022
Cited by 2 | Viewed by 2472
Abstract
Fertilization requires sperm migration toward oocytes and subsequent fusion. Sperm chemotaxis, a process in which motile sperm are attracted by factors released from oocytes or associated structures, plays a key role in sperm migration to oocytes. Here, we studied sperm chemotaxis in the [...] Read more.
Fertilization requires sperm migration toward oocytes and subsequent fusion. Sperm chemotaxis, a process in which motile sperm are attracted by factors released from oocytes or associated structures, plays a key role in sperm migration to oocytes. Here, we studied sperm chemotaxis in the nematode Ascaris suum. Our data show that uterus-derived factor (UDF), the protein fraction of uterine extracts, can attract spermatozoa. UDF is heat resistant, but its activity is attenuated by certain proteinases. UDF binds to the surface of spermatozoa but not spermatids, and this process is mediated by membranous organelles that fuse with the plasma membrane. UDF induces spermatozoa to release ATP from intracellular storage sites to the extracellular milieu, and extracellular ATP modulates sperm chemotaxis. Moreover, UDF increases protein serine phosphorylation (pS) levels in sperm, which facilitates sperm chemotaxis. Taken together, we revealed that both extracellular ATP and intracellular pS signaling are involved in Ascaris sperm chemotaxis. Our data provide insights into the mechanism of sperm chemotaxis in Ascaris suum. Full article
(This article belongs to the Section Molecular Biology)
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18 pages, 4354 KiB  
Article
Circ003429 Regulates Unsaturated Fatty Acid Synthesis in the Dairy Goat Mammary Gland by Interacting with miR-199a-3p, Targeting the YAP1 Gene
by Peixin Jiao, Meimei Zhang, Ziwei Wang, Gege Liang, Xiaolai Xie, Yonggen Zhang, Zhi Chen, Qianming Jiang and Juan J. Loor
Int. J. Mol. Sci. 2022, 23(7), 4068; https://doi.org/10.3390/ijms23074068 - 6 Apr 2022
Cited by 10 | Viewed by 2495
Abstract
Fatty acid composition is a key factor affecting the flavor and quality of goat milk. CircRNAs are now recognized as important regulators of transcription, and they play an important role in the control of fatty acid synthesis. Thus, understanding the regulatory mechanisms controlling [...] Read more.
Fatty acid composition is a key factor affecting the flavor and quality of goat milk. CircRNAs are now recognized as important regulators of transcription, and they play an important role in the control of fatty acid synthesis. Thus, understanding the regulatory mechanisms controlling this process in ruminant mammary glands is of great significance. In the present study, mammary tissue from dairy goats during early lactation and the dry period (nonlactating) were collected and used for high-throughput sequencing. Compared to levels during the dry period, the expression level of circ003429 during early lactation was lower (12.68-fold downregulated). In isolated goat mammary epithelial cells, circ003429 inhibited the synthesis of triglycerides (TAG) and decreased the content of unsaturated fatty acids (C16:1, C18:1, and C18:2), indicating that this circRNA plays an important role in regulating lipid synthesis. A binding site for miR-199a-3p in the circ003429 sequence was detected, and a dual-luciferase reporter system revealed that circ003429 targets miR-199a-3p. Overexpression of circ003429 (pcDNA-circ003429) downregulated the abundance of miR-199a-3p. In contrast, overexpression of miR-199a-3p increased TAG content and decreased mRNA abundance of Yes-associated protein 1 (YAP1) (a target gene of miR-199a-3p), and TAG content was decreased and mRNA abundance was increased in response to overexpression of circ003429. These results indicate that circ003429 alleviates the inhibitory effect of miR-199a-3p on the mRNA abundance of YAP1 by binding miR-199a-3p, resulting in subsequent regulation of the synthesis of TAG and unsaturated fatty acids. Full article
(This article belongs to the Special Issue Non-coding RNA Modification, Structure, Function and Application)
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16 pages, 2017 KiB  
Article
Luteolin Causes 5′CpG Demethylation of the Promoters of TSGs and Modulates the Aberrant Histone Modifications, Restoring the Expression of TSGs in Human Cancer Cells
by Sreepoorna Pramodh, Ritu Raina, Arif Hussain, Sali Abubaker Bagabir, Shafiul Haque, Syed Tasleem Raza, Mohammad Rehan Ajmal, Shalini Behl and Deepika Bhagavatula
Int. J. Mol. Sci. 2022, 23(7), 4067; https://doi.org/10.3390/ijms23074067 - 6 Apr 2022
Cited by 12 | Viewed by 3084
Abstract
Cancer progression is linked to abnormal epigenetic alterations such as DNA methylation and histone modifications. Since epigenetic alterations, unlike genetic changes, are heritable and reversible, they have been considered as interesting targets for cancer prevention and therapy by dietary compounds such as luteolin. [...] Read more.
Cancer progression is linked to abnormal epigenetic alterations such as DNA methylation and histone modifications. Since epigenetic alterations, unlike genetic changes, are heritable and reversible, they have been considered as interesting targets for cancer prevention and therapy by dietary compounds such as luteolin. In this study, epigenetic modulatory behaviour of luteolin was analysed on HeLa cells. Various assays including colony forming and migration assays, followed by biochemical assays of epigenetic enzymes including DNA methyltransferase, histone methyl transferase, histone acetyl transferase, and histone deacetylases assays were performed. Furthermore, global DNA methylation and methylation-specific PCR for examining the methylation status of CpG promoters of various tumour suppressor genes (TSGs) and the expression of these TSGs at transcript and protein level were performed. It was observed that luteolin inhibited migration and colony formation in HeLa cells. It also modulated DNA methylation at promoters of TSGs and the enzymatic activity of DNMT, HDAC, HMT, and HAT and reduced the global DNA methylation. Decrease in methylation resulted in the reactivation of silenced tumour suppressor genes including FHIT, DAPK1, PTEN, CDH1, SOCS1, TIMPS, VHL, TP53, TP73, etc. Hence, luteolin-targeted epigenetic alterations provide a promising approach for cancer prevention and intervention. Full article
(This article belongs to the Special Issue Impact of Natural Products on Glycation Linked Metabolic Disease)
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24 pages, 4000 KiB  
Article
IGFBP-3 Regulates Mitochondrial Hyperfusion and Metabolic Activity in Ocular Surface Epithelia during Hyperosmolar Stress
by Whitney L. Stuard, Melis K. Guner and Danielle M. Robertson
Int. J. Mol. Sci. 2022, 23(7), 4066; https://doi.org/10.3390/ijms23074066 - 6 Apr 2022
Cited by 3 | Viewed by 3719
Abstract
In the eye, hyperosmolarity of the precorneal tear film triggers inflammation and the development of dry eye disease (DED), a highly prevalent condition that causes depression and disability in severe forms. A member of the insulin-like growth factor (IGF) family, the IGF binding [...] Read more.
In the eye, hyperosmolarity of the precorneal tear film triggers inflammation and the development of dry eye disease (DED), a highly prevalent condition that causes depression and disability in severe forms. A member of the insulin-like growth factor (IGF) family, the IGF binding protein-3 (IGFBP-3), is a pleiotropic protein with known roles in growth downregulation and survival. IGFBP-3 exerts these effects by blocking IGF-1 activation of the type 1 IGF-receptor (IGF-1R). Here, we examined a new IGF-independent role for IGFBP-3 in the regulation of mitochondrial and metabolic activity in ocular surface epithelial cells subject to hyperosmolar stress and in a mouse model of DED. We found that hyperosmolar stress decreased IGFBP-3 expression in vitro and in vivo. Treatment with exogenous IGFBP-3 induced an early, transient shift in IGF-1R to mitochondria, followed by IGFBP-3 nuclear accumulation. IGFBP-3 nuclear accumulation increased protein translation, blocked the hyperosmolar-mediated decrease in oxidative phosphorylation through the induction of mitochondrial hyperfusion, and restored corneal health in vivo. These data indicate that IGFBP-3 acts a stress response protein in ocular surface epithelia subject to hyperosmolar stress. These findings may lead to the development of first-in-class therapeutics to treat eye diseases with underlying mitochondrial dysfunction. Full article
(This article belongs to the Special Issue Pathophysiologic Mechanisms of Eye Diseases and Novel Therapeutic Approaches)
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28 pages, 3178 KiB  
Review
The Use of Autologous Chondrocyte and Mesenchymal Stem Cell Implants for the Treatment of Focal Chondral Defects in Human Knee Joints—A Systematic Review and Meta-Analysis
by Ilias Ektor Epanomeritakis, Ernest Lee, Victor Lu and Wasim Khan
Int. J. Mol. Sci. 2022, 23(7), 4065; https://doi.org/10.3390/ijms23074065 - 6 Apr 2022
Cited by 20 | Viewed by 4666
Abstract
Focal chondral defects of the knee occur commonly in the young, active population due to trauma. Damage can insidiously spread and lead to osteoarthritis with significant functional and socioeconomic consequences. Implants consisting of autologous chondrocytes or mesenchymal stem cells (MSC) seeded onto scaffolds [...] Read more.
Focal chondral defects of the knee occur commonly in the young, active population due to trauma. Damage can insidiously spread and lead to osteoarthritis with significant functional and socioeconomic consequences. Implants consisting of autologous chondrocytes or mesenchymal stem cells (MSC) seeded onto scaffolds have been suggested as promising therapies to restore these defects. However, the degree of integration between the implant and native cartilage still requires optimization. A PRISMA systematic review and meta-analysis was conducted using five databases (PubMed, MEDLINE, EMBASE, Web of Science, CINAHL) to identify studies that used autologous chondrocyte implants (ACI) or MSC implant therapies to repair chondral defects of the tibiofemoral joint. Data on the integration of the implant-cartilage interface, as well as outcomes of clinical scoring systems, were extracted. Most eligible studies investigated the use of ACI only. Our meta-analysis showed that, across a total of 200 patients, 64% (95% CI (51%, 75%)) achieved complete integration with native cartilage. In addition, a pooled improvement in the mean MOCART integration score was observed during post-operative follow-up (standardized mean difference: 1.16; 95% CI (0.07, 2.24), p = 0.04). All studies showed an improvement in the clinical scores. The use of a collagen-based scaffold was associated with better integration and clinical outcomes. This review demonstrated that cell-seeded scaffolds can achieve good quality integration in most patients, which improves over time and is associated with clinical improvements. A greater number of studies comparing these techniques to traditional cartilage repair methods, with more inclusion of MSC-seeded scaffolds, should allow for a standardized approach to cartilage regeneration to develop. Full article
(This article belongs to the Section Molecular Biology)
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13 pages, 2252 KiB  
Article
The Growth, Lipid Accumulation and Fatty Acid Profile Analysis by Abscisic Acid and Indol-3-Acetic Acid Induced in Chlorella sp. FACHB-8
by Yihua Lin, Yue Dai, Weinan Xu, Xiaobin Wu, Yanyan Li, Hongmei Zhu and Hantao Zhou
Int. J. Mol. Sci. 2022, 23(7), 4064; https://doi.org/10.3390/ijms23074064 - 6 Apr 2022
Cited by 17 | Viewed by 3201
Abstract
Microalgae are considered a promising source for biodiesel. The addition of plant hormone can exert a significant impact on the production of microalgae biomass and lipid accumulation. Nevertheless, the response of microalgae cells to hormones is species- or strain-dependent. It remains controversial which [...] Read more.
Microalgae are considered a promising source for biodiesel. The addition of plant hormone can exert a significant impact on the production of microalgae biomass and lipid accumulation. Nevertheless, the response of microalgae cells to hormones is species- or strain-dependent. It remains controversial which genes involved in strong increase of fatty acids production in response to abscisic acid (ABA) in Chlorella sp. FACHB-8 strain. We investigated cell growth, lipid accumulation, and fatty acid composition when ABA and indol-3-acetic acid (IAA) were used in the growth medium of Chlorella sp. FACHB-8. The four treatments, including 5 mg/L IAA (E1), 10 mg/L IAA (E2), 10 mg/L ABA (E3), the combination of 5 mg/L IAA and 5 mg/L ABA (E4), were found to increase cell growth, but only 10 mg/L ABA treatment could enhance the lipid accumulation. The fatty acid profile was changed by the addition of ABA, making fatty acids afflux from polyunsaturated fatty acids to monounsaturated and saturated fatty acids, which were suitable for diesel application. Furthermore, a transcriptome analysis was conducted, unraveling the differentially expressed genes enriched in fatty acid biosynthesis, fatty acid metabolism, and biosynthesis of the unsaturated fatty acid pathway in response to ABA. Our results clarified the correlation of fatty acid synthesis-related genes and fatty acid profiles, helping understand the potential response mechanism of Chlorella sp. FACHB-8 strain respond to ABA treatment. Full article
(This article belongs to the Special Issue Abiotic Stress: Signaling and Responses)
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13 pages, 10441 KiB  
Article
In Vitro SARS-CoV-2 Infection of Microvascular Endothelial Cells: Effect on Pro-Inflammatory Cytokine and Chemokine Release
by Maria Dolci, Lucia Signorini, Sarah D’Alessandro, Federica Perego, Silvia Parapini, Michele Sommariva, Donatella Taramelli, Pasquale Ferrante, Nicoletta Basilico and Serena Delbue
Int. J. Mol. Sci. 2022, 23(7), 4063; https://doi.org/10.3390/ijms23074063 - 6 Apr 2022
Cited by 8 | Viewed by 2981
Abstract
In the novel pandemic of Coronavirus Disease 2019, high levels of pro-inflammatory cytokines lead to endothelial activation and dysfunction, promoting a pro-coagulative state, thrombotic events, and microvasculature injuries. The aim of the present work was to investigate the effect of SARS-CoV-2 on pro-inflammatory [...] Read more.
In the novel pandemic of Coronavirus Disease 2019, high levels of pro-inflammatory cytokines lead to endothelial activation and dysfunction, promoting a pro-coagulative state, thrombotic events, and microvasculature injuries. The aim of the present work was to investigate the effect of SARS-CoV-2 on pro-inflammatory cytokines, tissue factor, and chemokine release, with Human Microvascular Endothelial Cells (HMEC-1). ACE2 receptor expression was evaluated by western blot analysis. SARS-CoV-2 infection was assessed by one-step RT-PCR until 7 days post-infection (p.i.), and by Transmission Electron Microscopy (TEM). IL-6, TNF-α, IL-8, IFN-α, and hTF mRNA expression levels were detected by RT-PCR, while cytokine release was evaluated by ELISA. HMEC-1 expressed ACE2 receptor and SARS-CoV-2 infection showed a constant viral load. TEM analysis showed virions localized in the cytoplasm. Expression of IL-6 at 24 h and IFN-α mRNA at 24 h and 48 h p.i. was higher in infected than uninfected HMEC-1 (p < 0.05). IL-6 levels were significantly higher in supernatants from infected HMEC-1 (p < 0.001) at 24 h, 48 h, and 72 h p.i., while IL-8 levels were significantly lower at 24 h p.i. (p < 0.001). These data indicate that in vitro microvascular endothelial cells are susceptible to SARS-CoV-2 infection but slightly contribute to viral amplification. However, SARS-CoV-2 infection might trigger the increase of pro-inflammatory mediators. Full article
(This article belongs to the Section Molecular Immunology)
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16 pages, 4328 KiB  
Article
Drug-Free Nasal Spray as a Barrier against SARS-CoV-2 and Its Delta Variant: In Vitro Study of Safety and Efficacy in Human Nasal Airway Epithelia
by Fabio Fais, Reda Juskeviciene, Veronica Francardo, Stéphanie Mateos, Manuela Guyard, Cécile Viollet, Samuel Constant, Massimo Borelli and Ilja P. Hohenfeld
Int. J. Mol. Sci. 2022, 23(7), 4062; https://doi.org/10.3390/ijms23074062 - 6 Apr 2022
Cited by 11 | Viewed by 5659
Abstract
The nasal epithelium is a key portal for infection by respiratory viruses such as SARS-CoV-2 and represents an important target for prophylactic and therapeutic interventions. In the present study, we test the safety and efficacy of a newly developed nasal spray (AM-301, marketed [...] Read more.
The nasal epithelium is a key portal for infection by respiratory viruses such as SARS-CoV-2 and represents an important target for prophylactic and therapeutic interventions. In the present study, we test the safety and efficacy of a newly developed nasal spray (AM-301, marketed as Bentrio) against infection by SARS-CoV-2 and its Delta variant on an in vitro 3D-model of the primary human nasal airway epithelium. Safety was assessed in assays for tight junction integrity, cytotoxicity and cilia beating frequency. Efficacy against SARS-CoV-2 infection was evaluated in pre-viral load and post-viral load application on airway epithelium. No toxic effects of AM-301 on the nasal epithelium were found. Prophylactic treatment with AM-301 significantly reduced viral titer vs. controls over 4 days, reaching a maximum reduction of 99% in case of infection from the wild-type SARS-CoV-2 variant and more than 83% in case of the Delta variant. When AM-301 administration was started 24 h after infection, viral titer was reduced by about 12-folds and 3-folds on Day 4. The results suggest that AM-301 is safe and significantly decelerates SARS-CoV-2 replication in cell culture inhibition assays of prophylaxis (pre-viral load application) and mitigation (post-viral load application). Its physical (non-pharmaceutical) mechanism of action, safety and efficacy warrant additional investigations both in vitro and in vivo for safety and efficacy against a broad spectrum of airborne viruses and allergens. Full article
(This article belongs to the Special Issue Molecular Interactions and Mechanisms of COVID-19 Inhibition)
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20 pages, 8693 KiB  
Article
Time- and Spectrally-Resolved Photoluminescence Study of Alloyed CdxZn1−xSeyS1−y/ZnS Quantum Dots and Their Nanocomposites with SPIONs in Living Cells
by Anna Matiushkina, Ilia Litvinov, Anastasia Bazhenova, Tatiana Belyaeva, Aliaksei Dubavik, Andrei Veniaminov, Vladimir Maslov, Elena Kornilova and Anna Orlova
Int. J. Mol. Sci. 2022, 23(7), 4061; https://doi.org/10.3390/ijms23074061 - 6 Apr 2022
Cited by 4 | Viewed by 2695
Abstract
Magnetic-luminescent composites based on semiconductor quantum dots (QDs) and superparamagnetic iron oxide nanoparticles (SPIONs) can serve as a platform combining visualization and therapy. Here, we report the construction of QD-SPION nanocomposites based on synthesized SPIONs and alloyed QDs [...] Read more.
Magnetic-luminescent composites based on semiconductor quantum dots (QDs) and superparamagnetic iron oxide nanoparticles (SPIONs) can serve as a platform combining visualization and therapy. Here, we report the construction of QD-SPION nanocomposites based on synthesized SPIONs and alloyed QDs (CdxZn1−xSeyS1−y)/ZnS solubilized with L-cysteine molecules. The study of the spectral-luminescence characteristics, the kinetics of luminescence decay show the composite’s stability in a solution. After incubation with HeLa cells, QDs, SPIONs, and their composites form clusters on the cell surface and associate with endosomes inside the cells. Component-wise analysis of the photoluminescence decay of cell-associated QDs/SPIONs provides information about their localization and aggregate status. Full article
(This article belongs to the Special Issue Nano-Materials and Methods 3.0)
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15 pages, 4601 KiB  
Article
BRCA2 C-Terminal RAD51-Binding Domain Confers Resistance to DNA-Damaging Agents
by Zida Zhu, Taisuke Kitano, Masami Morimatsu, Arisa Tanaka, Ryo Morioka, Xianghui Lin, Koichi Orino and Yasunaga Yoshikawa
Int. J. Mol. Sci. 2022, 23(7), 4060; https://doi.org/10.3390/ijms23074060 - 6 Apr 2022
Viewed by 2711
Abstract
Breast cancer type 2 susceptibility (BRCA2) protein is crucial for initiating DNA damage repair after chemotherapy with DNA interstrand crosslinking agents or X-ray irradiation, which induces DNA double-strand breaks. BRCA2 contains a C-terminal RAD51-binding domain (CTRBD) that interacts with RAD51 oligomer-containing nucleofilaments. In [...] Read more.
Breast cancer type 2 susceptibility (BRCA2) protein is crucial for initiating DNA damage repair after chemotherapy with DNA interstrand crosslinking agents or X-ray irradiation, which induces DNA double-strand breaks. BRCA2 contains a C-terminal RAD51-binding domain (CTRBD) that interacts with RAD51 oligomer-containing nucleofilaments. In this study, we investigated CTRBD expression in cells exposed to X-ray irradiation and mitomycin C treatment. Surprisingly, BRCA2 CTRBD expression in HeLa cells increased their resistance to X-ray irradiation and mitomycin C. Under endogenous BRCA2 depletion using shRNA, the sensitivities of the BRCA2-depleted cells with and without the CTRBD did not significantly differ. Thus, the resistance to X-ray irradiation conferred by an exogenous CTRBD required endogenous BRCA2 expression. BRCA2 CTRBD-expressing cells demonstrated effective RAD51 foci formation and increased homologous recombination efficiency, but not nonhomologous end-joining efficiency. To the best of our knowledge, our study is the first to report the ability of the BRCA2 functional domain to confer resistance to X-ray irradiation and mitomycin C treatment by increased homologous recombination efficiency. Thus, this peptide may be useful for protecting cells against X-ray irradiation or chemotherapeutic agents. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Biology and Medicine)
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15 pages, 5419 KiB  
Article
Direct Reprogramming and Induction of Human Dermal Fibroblasts to Differentiate into iPS-Derived Nucleus Pulposus-like Cells in 3D Culture
by Shoji Seki, Mami Iwasaki, Hiroto Makino, Yasuhito Yahara, Yoshitaka Miyazaki, Katsuhiko Kamei, Hayato Futakawa, Makiko Nogami, Nguyen Tran Canh Tung, Tatsuro Hirokawa, Mamiko Tsuji and Yoshiharu Kawaguchi
Int. J. Mol. Sci. 2022, 23(7), 4059; https://doi.org/10.3390/ijms23074059 - 6 Apr 2022
Cited by 5 | Viewed by 3045
Abstract
Intervertebral disc (IVD) diseases are common spinal disorders that cause neck or back pain in the presence or absence of an underlying neurological disorder. IVD diseases develop on the basis of degeneration, and there are no established treatments for degeneration. IVD diseases may [...] Read more.
Intervertebral disc (IVD) diseases are common spinal disorders that cause neck or back pain in the presence or absence of an underlying neurological disorder. IVD diseases develop on the basis of degeneration, and there are no established treatments for degeneration. IVD diseases may therefore represent a candidate for the application of regenerative medicine, potentially employing normal human dermal fibroblasts (NHDFs) induced to differentiate into nucleus pulposus (NP) cells. Here, we used a three-dimensional culture system to demonstrate that ectopic expression of MYC, KLF4, NOTO, SOX5, SOX6, and SOX9 in NHDFs generated NP-like cells, detected using Safranin-O staining. Quantitative PCR, microarray analysis, and fluorescence-activated cell sorting revealed that the induced NP cells exhibited a fully differentiated phenotype. These findings may significantly contribute to the development of effective strategies for treating IVD diseases. Full article
(This article belongs to the Special Issue Regeneration for Spinal Diseases 2.0)
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14 pages, 2931 KiB  
Article
Protein Profiling of WERI-RB1 and Etoposide-Resistant WERI-ETOR Reveals New Insights into Topoisomerase Inhibitor Resistance in Retinoblastoma
by Vinodh Kakkassery, Timo Gemoll, Miriam M. Kraemer, Thorben Sauer, Aysegül Tura, Mahdy Ranjbar, Salvatore Grisanti, Stephanie C. Joachim, Stefan Mergler and Jacqueline Reinhard
Int. J. Mol. Sci. 2022, 23(7), 4058; https://doi.org/10.3390/ijms23074058 - 6 Apr 2022
Cited by 6 | Viewed by 3143
Abstract
Chemotherapy resistance is one of the reasons for eye loss in patients with retinoblastoma (RB). RB chemotherapy resistance has been studied in different cell culture models, such as WERI-RB1. In addition, chemotherapy-resistant RB subclones, such as the etoposide-resistant WERI-ETOR cell line have been [...] Read more.
Chemotherapy resistance is one of the reasons for eye loss in patients with retinoblastoma (RB). RB chemotherapy resistance has been studied in different cell culture models, such as WERI-RB1. In addition, chemotherapy-resistant RB subclones, such as the etoposide-resistant WERI-ETOR cell line have been established to improve the understanding of chemotherapy resistance in RB. The objective of this study was to characterize cell line models of an etoposide-sensitive WERI-RB1 and its etoposide-resistant subclone, WERI-ETOR, by proteomic analysis. Subsequently, quantitative proteomics data served for correlation analysis with known drug perturbation profiles. Methodically, WERI-RB1 and WERI-ETOR were cultured, and prepared for quantitative mass spectrometry (MS). This was carried out in a data-independent acquisition (DIA) mode. The raw SWATH (sequential window acquisition of all theoretical mass spectra) files were processed using neural networks in a library-free mode along with machine-learning algorithms. Pathway-enrichment analysis was performed using the REACTOME-pathway resource, and correlated to the molecular signature database (MSigDB) hallmark gene set collections for functional annotation. Furthermore, a drug-connectivity analysis using the L1000 database was carried out to associate the mechanism of action (MOA) for different anticancer reagents to WERI-RB1/WERI-ETOR signatures. A total of 4756 proteins were identified across all samples, showing a distinct clustering between the groups. Of these proteins, 64 were significantly altered (q < 0.05 & log2FC |>2|, 22 higher in WERI-ETOR). Pathway analysis revealed the “retinoid metabolism and transport” pathway as an enriched metabolic pathway in WERI-ETOR cells, while the “sphingolipid de novo biosynthesis” pathway was identified in the WERI-RB1 cell line. In addition, this study revealed similar protein signatures of topoisomerase inhibitors in WERI-ETOR cells as well as ATPase inhibitors, acetylcholine receptor antagonists, and vascular endothelial growth factor receptor (VEGFR) inhibitors in the WERI-RB1 cell line. In this study, WERI-RB1 and WERI-ETOR were analyzed as a cell line model for chemotherapy resistance in RB using data-independent MS. Analysis of the global proteome identified activation of “sphingolipid de novo biosynthesis” in WERI-RB1, and revealed future potential treatment options for etoposide resistance in RB. Full article
(This article belongs to the Special Issue Primary Intraocular Tumors–Molecular Mechanisms, Novel Therapeutic Strategies and Targets)
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13 pages, 1340 KiB  
Article
Antinociceptive and Antiallodynic Activity of Some 3-(3-Methylthiophen-2-yl)pyrrolidine-2,5-dione Derivatives in Mouse Models of Tonic and Neuropathic Pain
by Anna Dziubina, Anna Rapacz, Anna Czopek, Małgorzata Góra, Jolanta Obniska and Krzysztof Kamiński
Int. J. Mol. Sci. 2022, 23(7), 4057; https://doi.org/10.3390/ijms23074057 - 6 Apr 2022
Cited by 2 | Viewed by 2261
Abstract
Antiseizure drugs (ASDs) are commonly used to treat a wide range of nonepileptic conditions, including pain. In this context, the analgesic effect of four pyrrolidine-2,5-dione derivatives (compounds 3, 4, 6, and 9), with previously confirmed anticonvulsant and preliminary antinociceptive [...] Read more.
Antiseizure drugs (ASDs) are commonly used to treat a wide range of nonepileptic conditions, including pain. In this context, the analgesic effect of four pyrrolidine-2,5-dione derivatives (compounds 3, 4, 6, and 9), with previously confirmed anticonvulsant and preliminary antinociceptive activity, was assessed in established pain models. Consequently, antinociceptive activity was examined in a mouse model of tonic pain (the formalin test). In turn, antiallodynic and antihyperalgesic activity were examined in the oxaliplatin-induced model of peripheral neuropathy as well as in the streptozotocin-induced model of painful diabetic neuropathy in mice. In order to assess potential sedative properties (drug safety evaluation), the influence on locomotor activity was also investigated. As a result, three compounds, namely 3, 6, and 9, demonstrated a significant antinociceptive effect in the formalin-induced model of tonic pain. Furthermore, these substances also revealed antiallodynic properties in the model of oxaliplatin-induced peripheral neuropathy, while compound 3 attenuated tactile allodynia in the model of diabetic streptozotocin-induced peripheral neuropathy. Apart from favorable analgesic properties, the most active compound 3 did not induce any sedative effects at the active dose of 30 mg/kg after intraperitoneal (i.p.) injection. Full article
(This article belongs to the Special Issue Heterocyclic Compounds: Advanced Syntheses and Applications)
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15 pages, 4412 KiB  
Article
The Effects of Chimeric Antigen Receptor (CAR) Hinge Domain Post-Translational Modifications on CAR-T Cell Activity
by Sachiko Hirobe, Keisuke Imaeda, Masashi Tachibana and Naoki Okada
Int. J. Mol. Sci. 2022, 23(7), 4056; https://doi.org/10.3390/ijms23074056 - 6 Apr 2022
Cited by 11 | Viewed by 3414
Abstract
To improve the efficacy and safety of chimeric antigen receptor (CAR)-expressing T cell therapeutics through enhanced CAR design, we analysed CAR structural factors that affect CAR-T cell function. We studied the effects of disulphide bonding at cysteine residues and glycosylation in the HD [...] Read more.
To improve the efficacy and safety of chimeric antigen receptor (CAR)-expressing T cell therapeutics through enhanced CAR design, we analysed CAR structural factors that affect CAR-T cell function. We studied the effects of disulphide bonding at cysteine residues and glycosylation in the HD on CAR-T function. We used first-generation CAR[V/28/28/3z] and CAR[V/8a/8a/3z], consisting of a mouse vascular endothelial growth factor receptor 2 (VEGFR2)-specific single-chain variable fragment tandemly linked to CD28- or CD8α-derived HD, transmembrane domain (TMD) and a CD3ζ-derived signal transduction domain (STD). We constructed structural variants by substituting cysteine with alanine and asparagine (putative N-linked glycosylation sites) with aspartate. CAR[V/28/28/3z] and CAR[V/8a/8a/3z] formed homodimers, the former through a single HD cysteine residue and the latter through the more TMD-proximal of the two cysteine residues. The absence of disulphide bonds did not affect membrane CAR expression but reduced antigen-specific cytokine production and cytotoxic activity. CAR[V/28/28/3z] and CAR[V/8a/8a/3z] harboured one N-linked glycosylation site, and CAR[V/8a/8a/3z] underwent considerable O-linked glycosylation at an unknown site. Thus, N-linked glycosylation of CAR[V/28/28/3z] promotes stable membrane CAR expression, while having no effect on the expression or CAR-T cell activity of CAR[V/8a/8a/3z]. Our findings demonstrate that post-translational modifications of the CAR HD influence CAR-T cell activity, establishing a basis for future CAR design. Full article
(This article belongs to the Special Issue Similarities and Differences between Chimeric Antigen Receptor and T Cell Receptor Signaling)
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17 pages, 2799 KiB  
Review
Physical Forces in Glioblastoma Migration: A Systematic Review
by Audrey Grossen, Kyle Smith, Nangorgo Coulibaly, Benjamin Arbuckle, Alexander Evans, Stefan Wilhelm, Kenneth Jones, Ian Dunn, Rheal Towner, Dee Wu, Young-Tae Kim and James Battiste
Int. J. Mol. Sci. 2022, 23(7), 4055; https://doi.org/10.3390/ijms23074055 - 6 Apr 2022
Cited by 9 | Viewed by 3808
Abstract
The invasive capabilities of glioblastoma (GBM) define the cancer’s aggressiveness, treatment resistance, and overall mortality. The tumor microenvironment influences the molecular behavior of cells, both epigenetically and genetically. Current forces being studied include properties of the extracellular matrix (ECM), such as stiffness and [...] Read more.
The invasive capabilities of glioblastoma (GBM) define the cancer’s aggressiveness, treatment resistance, and overall mortality. The tumor microenvironment influences the molecular behavior of cells, both epigenetically and genetically. Current forces being studied include properties of the extracellular matrix (ECM), such as stiffness and “sensing” capabilities. There is currently limited data on the physical forces in GBM—both relating to how they influence their environment and how their environment influences them. This review outlines the advances that have been made in the field. It is our hope that further investigation of the physical forces involved in GBM will highlight new therapeutic options and increase patient survival. A search of the PubMed database was conducted through to 23 March 2022 with the following search terms: (glioblastoma) AND (physical forces OR pressure OR shear forces OR compression OR tension OR torsion) AND (migration OR invasion). Our review yielded 11 external/applied/mechanical forces and 2 tumor microenvironment (TME) forces that affect the ability of GBM to locally migrate and invade. Both external forces and forces within the tumor microenvironment have been implicated in GBM migration, invasion, and treatment resistance. We endorse further research in this area to target the physical forces affecting the migration and invasion of GBM. Full article
(This article belongs to the Special Issue Novel Players in Chemioresistance as New Targets for Cancer Treatment)
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26 pages, 7287 KiB  
Article
Cloning and Organelle Expression of Bamboo Mitochondrial Complex I Subunits Nad1, Nad2, Nad4, and Nad5 in the Yeast Saccharomyces cerevisiae
by Hsieh-Chin Tsai, Cheng-Hung Hsieh, Ching-Wen Hsu, Yau-Heiu Hsu and Lee-Feng Chien
Int. J. Mol. Sci. 2022, 23(7), 4054; https://doi.org/10.3390/ijms23074054 - 6 Apr 2022
Cited by 4 | Viewed by 2661
Abstract
Mitochondrial respiratory complex I catalyzes electron transfer from NADH to ubiquinone and pumps protons from the matrix into the intermembrane space. In particular, the complex I subunits Nad1, Nad2, Nad4, and Nad5, which are encoded by the nad1, nad2, nad4, [...] Read more.
Mitochondrial respiratory complex I catalyzes electron transfer from NADH to ubiquinone and pumps protons from the matrix into the intermembrane space. In particular, the complex I subunits Nad1, Nad2, Nad4, and Nad5, which are encoded by the nad1, nad2, nad4, and nad5 genes, reside at the mitochondrial inner membrane and possibly function as proton (H+) and ion translocators. To understand the individual functional roles of the Nad1, Nad2, Nad4, and Nad5 subunits in bamboo, each cDNA of these four genes was cloned into the pYES2 vector and expressed in the mitochondria of the yeast Saccharomyces cerevisiae. The mitochondrial targeting peptide mt gene (encoding MT) and the egfp marker gene (encoding enhanced green fluorescent protein, EGFP) were fused at the 5′-terminal and 3′-terminal ends, respectively. The constructed plasmids were then transformed into yeast. RNA transcripts and fusion protein expression were observed in the yeast transformants. Mitochondrial localizations of the MT-Nad1-EGFP, MT-Nad2-EGFP, MT-Nad4-EGFP, and MT-Nad5-EGFP fusion proteins were confirmed by fluorescence microscopy. The ectopically expressed bamboo subunits Nad1, Nad2, Nad4, and Nad5 may function in ion translocation, which was confirmed by growth phenotype assays with the addition of different concentrations of K+, Na+, or H+. Full article
(This article belongs to the Section Molecular Plant Sciences)
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20 pages, 1923 KiB  
Article
shRNAs Targeting a Common KCNQ1 Variant Could Alleviate Long-QT1 Disease Severity by Inhibiting a Mutant Allele
by Lucía Cócera-Ortega, Ronald Wilders, Selina C. Kamps, Benedetta Fabrizi, Irit Huber, Ingeborg van der Made, Anouk van den Bout, Dylan K. de Vries, Lior Gepstein, Arie O. Verkerk, Yigal M. Pinto and Anke J. Tijsen
Int. J. Mol. Sci. 2022, 23(7), 4053; https://doi.org/10.3390/ijms23074053 - 6 Apr 2022
Cited by 2 | Viewed by 3526
Abstract
Long-QT syndrome type 1 (LQT1) is caused by mutations in KCNQ1. Patients heterozygous for such a mutation co-assemble both mutant and wild-type KCNQ1-encoded subunits into tetrameric Kv7.1 potassium channels. Here, we investigated whether allele-specific inhibition of mutant KCNQ1 by targeting a [...] Read more.
Long-QT syndrome type 1 (LQT1) is caused by mutations in KCNQ1. Patients heterozygous for such a mutation co-assemble both mutant and wild-type KCNQ1-encoded subunits into tetrameric Kv7.1 potassium channels. Here, we investigated whether allele-specific inhibition of mutant KCNQ1 by targeting a common variant can shift the balance towards increased incorporation of the wild-type allele to alleviate the disease in human-induced pluripotent stem-cell-derived cardiomyocytes (hiPSC-CMs). We identified the single nucleotide polymorphisms (SNP) rs1057128 (G/A) in KCNQ1, with a heterozygosity of 27% in the European population. Next, we determined allele-specificity of short-hairpin RNAs (shRNAs) targeting either allele of this SNP in hiPSC-CMs that carry an LQT1 mutation. Our shRNAs downregulated 60% of the A allele and 40% of the G allele without affecting the non-targeted allele. Suppression of the mutant KCNQ1 allele by 60% decreased the occurrence of arrhythmic events in hiPSC-CMs measured by a voltage-sensitive reporter, while suppression of the wild-type allele increased the occurrence of arrhythmic events. Furthermore, computer simulations based on another LQT1 mutation revealed that 60% suppression of the mutant KCNQ1 allele shortens the prolonged action potential in an adult cardiomyocyte model. We conclude that allele-specific inhibition of a mutant KCNQ1 allele by targeting a common variant may alleviate the disease. This novel approach avoids the need to design shRNAs to target every single mutation and opens up the exciting possibility of treating multiple LQT1-causing mutations with only two shRNAs. Full article
(This article belongs to the Special Issue The Magnificent World of Induced Pluripotent Stem Cell-Derived Cardiomyocytes)
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19 pages, 6357 KiB  
Article
1,2,3,4,6-Penta-O-galloyl-d-glucose Interrupts the Early Adipocyte Lifecycle and Attenuates Adiposity and Hepatic Steatosis in Mice with Diet-Induced Obesity
by Ashish Rao Sathyanarayana, Chung-Kuang Lu, Chih-Chuang Liaw, Chia-Chuan Chang, Hsin-Ying Han, Brian D. Green, Wei-Jan Huang, Cheng Huang, Wen-Di He, Lin-Chien Lee and Hui-Kang Liu
Int. J. Mol. Sci. 2022, 23(7), 4052; https://doi.org/10.3390/ijms23074052 - 6 Apr 2022
Cited by 7 | Viewed by 3092
Abstract
Phytochemicals that interrupt adipocyte lifecycle can provide anti-obesity effects. 1,2,3,4,6-penta-O-galloyl-d-glucose (PGG) is a tannin with two isomers that occurs widely in plants and exhibits various pharmacological activities. The aim of the investigation is to comprehensively examine effects of PGG isomer(s) on [...] Read more.
Phytochemicals that interrupt adipocyte lifecycle can provide anti-obesity effects. 1,2,3,4,6-penta-O-galloyl-d-glucose (PGG) is a tannin with two isomers that occurs widely in plants and exhibits various pharmacological activities. The aim of the investigation is to comprehensively examine effects of PGG isomer(s) on adipocyte lifecycle and diet-induced obesity. Human mesenchymal stem cells (hMSC), 3T3-L1 fibroblasts, and H4IIE hepatoma cells were used to determine the effects of PGG isomers on cell viability and adipogenesis. Mice with diet-induced obesity were generated from male C57/BL6 mice fed with a 45% high fat diet. Oral administration of β-PGG (0.1 and 5 mg/kg) lasted for 14 weeks. Viability was reduced by repeated PGG treatment in hMSC, preadipocytes, and cells under differentiation. PGG mainly induces apoptosis, and this effect is independent of its insulin mimetic action. In vivo, administration of β-PGG attenuated shortening of the colon, hyperlipidaemia, fat cells and islet hypertrophy in DIO mice. Hepatic steatosis and related gene expression were improved along with glucose intolerance. Increased serum adiponectin, leptin, and glucagon-like peptide-1 levels were also observed. In conclusion, repeated PGG treatment interrupts the adipocyte lifecycle. PGG administration reduces adiposity and fatty liver development in DIO mice, and therefore, PGG could aid in clinical management of obesity. Full article
(This article belongs to the Collection Feature Papers in Molecular Toxicology)
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23 pages, 2690 KiB  
Article
Nitric Oxide Implication in Potato Immunity to Phytophthora infestans via Modifications of Histone H3/H4 Methylation Patterns on Defense Genes
by Andżelika Drozda, Barbara Kurpisz, Magdalena Arasimowicz-Jelonek, Daniel Kuźnicki, Przemysław Jagodzik, Yufeng Guan and Jolanta Floryszak-Wieczorek
Int. J. Mol. Sci. 2022, 23(7), 4051; https://doi.org/10.3390/ijms23074051 - 6 Apr 2022
Cited by 7 | Viewed by 2927
Abstract
Nitric oxide (NO) is an essential redox-signaling molecule operating in many physiological and pathophysiological processes. However, evidence on putative NO engagement in plant immunity by affecting defense gene expressions, including histone modifications, is poorly recognized. Exploring the effect of biphasic NO generation regulated [...] Read more.
Nitric oxide (NO) is an essential redox-signaling molecule operating in many physiological and pathophysiological processes. However, evidence on putative NO engagement in plant immunity by affecting defense gene expressions, including histone modifications, is poorly recognized. Exploring the effect of biphasic NO generation regulated by S-nitrosoglutathione reductase (GNSOR) activity after avr Phytophthora infestans inoculation, we showed that the phase of NO decline at 6 h post-inoculation (hpi) was correlated with the rise of defense gene expressions enriched in the TrxG-mediated H3K4me3 active mark in their promoter regions. Here, we report that arginine methyltransferase PRMT5 catalyzing histone H4R3 symmetric dimethylation (H4R3sme2) is necessary to ensure potato resistance to avr P. infestans. Both the pathogen and S-nitrosoglutathione (GSNO) altered the methylation status of H4R3sme2 by transient reduction in the repressive mark in the promoter of defense genes, R3a and HSR203J (a resistance marker), thereby elevating their transcription. In turn, the PRMT5-selective inhibitor repressed R3a expression and attenuated the hypersensitive response to the pathogen. In conclusion, we postulate that lowering the NO level (at 6 hpi) might be decisive for facilitating the pathogen-induced upregulation of stress genes via histone lysine methylation and PRMT5 controlling potato immunity to late blight. Full article
(This article belongs to the Special Issue Advanced Research in Plant Responses to Environmental Stresses 2.0)
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15 pages, 3612 KiB  
Article
Identification of Entry Inhibitors against Delta and Omicron Variants of SARS-CoV-2
by Richard Kuan-Lin Lee, Tian-Neng Li, Sui-Yuan Chang, Tai-Ling Chao, Chun-Hsien Kuo, Max Yu-Chen Pan, Yu-Ting Chiou, Kuan-Ju Liao, Yi Yang, Yi-Hsuan Wu, Chen-Hao Huang, Hsueh-Fen Juan, Hsing-Pang Hsieh and Lily Hui-Ching Wang
Int. J. Mol. Sci. 2022, 23(7), 4050; https://doi.org/10.3390/ijms23074050 - 6 Apr 2022
Cited by 19 | Viewed by 5649
Abstract
Entry inhibitors against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgently needed to control the outbreak of coronavirus disease 2019 (COVID-19). This study developed a robust and straightforward assay that detected the molecular interaction between the receptor-binding domain (RBD) of viral spike [...] Read more.
Entry inhibitors against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgently needed to control the outbreak of coronavirus disease 2019 (COVID-19). This study developed a robust and straightforward assay that detected the molecular interaction between the receptor-binding domain (RBD) of viral spike protein and the angiotensin-converting enzyme 2 (ACE2) receptor in just 10 min. A drug library of 1068 approved compounds was used to screen for SARS-CoV2 entry inhibition, and 9 active drugs were identified as specific pseudovirus entry inhibitors. A plaque reduction neutralization test using authentic SARS-CoV-2 virus in Vero E6 cells confirmed that 2 of these drugs (Etravirine and Dolutegravir) significantly inhibited the infection of SARS-CoV-2. With molecular docking, we showed that both Etravirine and Dolutegravir are preferentially bound to primary ACE2-interacting residues on the RBD domain, implying that these two drug blocks may prohibit the viral attachment of SARS-CoV-2. We compared the neutralizing activities of these entry inhibitors against different pseudoviruses carrying spike proteins from alpha, beta, gamma, and delta variants. Both Etravirine and Dolutegravir showed similar neutralizing activities against different variants, with EC50 values between 4.5 to 5.8 nM for Etravirine and 10.2 to 22.9 nM for Dolutegravir. These data implied that Etravirine and Dolutegravir may serve as general spike inhibitors against dominant viral variants of SARS-CoV-2. Full article
(This article belongs to the Topic Acute Respiratory Viruses Molecular Epidemiology)
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14 pages, 1672 KiB  
Article
Validation and Data-Integration of Yeast-Based Assays for Functional Classification of BRCA1 Missense Variants
by Francesca Bellè, Alberto Mercatanti, Samuele Lodovichi, Caterina Congregati, Chiara Guglielmi, Mariella Tancredi, Maria Adelaide Caligo, Tiziana Cervelli and Alvaro Galli
Int. J. Mol. Sci. 2022, 23(7), 4049; https://doi.org/10.3390/ijms23074049 - 6 Apr 2022
Cited by 4 | Viewed by 2528
Abstract
Germline mutations in the BRCA1 gene have been reported to increase the lifetime risk of developing breast and/or ovarian cancer (BOC). By new sequencing technologies, numerous variants of uncertain significance (VUS) are identified. It is mandatory to develop new tools to evaluate their [...] Read more.
Germline mutations in the BRCA1 gene have been reported to increase the lifetime risk of developing breast and/or ovarian cancer (BOC). By new sequencing technologies, numerous variants of uncertain significance (VUS) are identified. It is mandatory to develop new tools to evaluate their functional impact and pathogenicity. As the expression of pathogenic BRCA1 variants in Saccharomyces cerevisiae increases the frequency of intra- and inter-chromosomal homologous recombination (HR), and gene reversion (GR), we validated the two HR and the GR assays by testing 23 benign and 23 pathogenic variants and compared the results with those that were obtained in the small colony phenotype (SCP) assay, an additional yeast-based assay, that was validated previously. We demonstrated that they scored high accuracy, sensitivity, and sensibility. By using a classifier that was based on majority of voting, we have integrated data from HR, GR, and SCP assays and developed a reliable method, named yBRCA1, with high sensitivity to obtain an accurate VUS functional classification (benign or pathogenic). The classification of BRCA1 variants, important for assessing the risk of developing BOC, is often difficult to establish with genetic methods because they occur rarely in the population. This study provides a new tool to get insights on the functional impact of the BRCA1 variants. Full article
(This article belongs to the Special Issue The Functional Impact of DNA Repair Gene Variants in Breast and Ovarian Cancer)
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17 pages, 1315 KiB  
Review
Biochemical Functions and Clinical Characterizations of the Sirtuins in Diabetes-Induced Retinal Pathologies
by Samanta Taurone, Chiara De Ponte, Dante Rotili, Elena De Santis, Antonello Mai, Francesco Fiorentino, Susanna Scarpa, Marco Artico and Alessandra Micera
Int. J. Mol. Sci. 2022, 23(7), 4048; https://doi.org/10.3390/ijms23074048 - 6 Apr 2022
Cited by 13 | Viewed by 2944
Abstract
Diabetic retinopathy (DR) is undoubtedly one of the most prominent causes of blindness worldwide. This pathology is the most frequent microvascular complication arising from diabetes, and its incidence is increasing at a constant pace. To date, the insurgence of DR is thought to [...] Read more.
Diabetic retinopathy (DR) is undoubtedly one of the most prominent causes of blindness worldwide. This pathology is the most frequent microvascular complication arising from diabetes, and its incidence is increasing at a constant pace. To date, the insurgence of DR is thought to be the consequence of the intricate complex of relations connecting inflammation, the generation of free oxygen species, and the consequent oxidative stress determined by protracted hyperglycemia. The sirtuin (SIRT) family comprises 7 histone and non-histone protein deacetylases and mono (ADP-ribosyl) transferases regulating different processes, including metabolism, senescence, DNA maintenance, and cell cycle regulation. These enzymes are involved in the development of various diseases such as neurodegeneration, cardiovascular pathologies, metabolic disorders, and cancer. SIRT1, 3, 5, and 6 are key enzymes in DR since they modulate glucose metabolism, insulin sensitivity, and inflammation. Currently, indirect and direct activators of SIRTs (such as antagomir, glycyrrhizin, and resveratrol) are being developed to modulate the inflammation response arising during DR. In this review, we aim to illustrate the most important inflammatory and metabolic pathways connecting SIRT activity to DR, and to describe the most relevant SIRT activators that might be proposed as new therapeutics to treat DR. Full article
(This article belongs to the Special Issue Immune Pathogenesis and Regulation of Ocular Inflammation)
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19 pages, 1551 KiB  
Review
Metabolic Syndrome and β-Oxidation of Long-Chain Fatty Acids in the Brain, Heart, and Kidney Mitochondria
by Alexander Panov, Vladimir I. Mayorov and Sergey Dikalov
Int. J. Mol. Sci. 2022, 23(7), 4047; https://doi.org/10.3390/ijms23074047 - 6 Apr 2022
Cited by 17 | Viewed by 4731
Abstract
We present evidence that metabolic syndrome (MetS) represents the postreproductive stage of the human postembryonic ontogenesis. Accordingly, the genes governing this stage experience relatively weak evolutionary selection pressure, thus representing the metabolic phenotype of distant ancestors with β-oxidation of long-chain fatty acids (FAs) [...] Read more.
We present evidence that metabolic syndrome (MetS) represents the postreproductive stage of the human postembryonic ontogenesis. Accordingly, the genes governing this stage experience relatively weak evolutionary selection pressure, thus representing the metabolic phenotype of distant ancestors with β-oxidation of long-chain fatty acids (FAs) as the primary energy source. Mitochondria oxidize at high-rate FAs only when succinate, glutamate, or pyruvate are present. The heart and brain mitochondria work at a wide range of functional loads and possess an intrinsic inhibition of complex II to prevent oxidative stress at periods of low functional activity. Kidney mitochondria constantly work at a high rate and lack inhibition of complex II. We suggest that in people with MetS, oxidative stress is the central mechanism of the heart and brain pathologies. Oxidative stress is a secondary pathogenetic mechanism in the kidney, while the primary mechanisms are kidney hypoxia caused by persistent hyperglycemia and hypertension. Current evidence suggests that most of the nongenetic pathologies associated with MetS originate from the inconsistencies between the metabolic phenotype acquired after the transition to the postreproductive stage and excessive consumption of food rich in carbohydrates and a sedentary lifestyle. Full article
(This article belongs to the Special Issue Mitochondria: Aging, Metabolic Syndrome and Cardiovascular Diseases)
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24 pages, 6512 KiB  
Article
Required Elements in tRNA for Methylation by the Eukaryotic tRNA (Guanine-N2-) Methyltransferase (Trm11-Trm112 Complex)
by Yu Nishida, Shiho Ohmori, Risa Kakizono, Kunpei Kawai, Miyu Namba, Kazuki Okada, Ryota Yamagami, Akira Hirata and Hiroyuki Hori
Int. J. Mol. Sci. 2022, 23(7), 4046; https://doi.org/10.3390/ijms23074046 - 6 Apr 2022
Cited by 5 | Viewed by 2456
Abstract
The Saccharomyces cerevisiae Trm11 and Trm112 complex (Trm11-Trm112) methylates the 2-amino group of guanosine at position 10 in tRNA and forms N2-methylguanosine. To determine the elements required in tRNA for methylation by Trm11-Trm112, we prepared 60 tRNA transcript variants and tested [...] Read more.
The Saccharomyces cerevisiae Trm11 and Trm112 complex (Trm11-Trm112) methylates the 2-amino group of guanosine at position 10 in tRNA and forms N2-methylguanosine. To determine the elements required in tRNA for methylation by Trm11-Trm112, we prepared 60 tRNA transcript variants and tested them for methylation by Trm11-Trm112. The results show that the precursor tRNA is not a substrate for Trm11-Trm112. Furthermore, the CCA terminus is essential for methylation by Trm11-Trm112, and Trm11-Trm112 also only methylates tRNAs with a regular-size variable region. In addition, the G10-C25 base pair is required for methylation by Trm11-Trm112. The data also demonstrated that Trm11-Trm112 recognizes the anticodon-loop and that U38 in tRNAAla acts negatively in terms of methylation. Likewise, the U32-A38 base pair in tRNACys negatively affects methylation. The only exception in our in vitro study was tRNAValAAC1. Our experiments showed that the tRNAValAAC1 transcript was slowly methylated by Trm11-Trm112. However, position 10 in this tRNA was reported to be unmodified G. We purified tRNAValAAC1 from wild-type and trm11 gene deletion strains and confirmed that a portion of tRNAValAAC1 is methylated by Trm11-Trm112 in S. cerevisiae. Thus, our study explains the m2G10 modification pattern of all S. cerevisiae class I tRNAs and elucidates the Trm11-Trm112 binding sites. Full article
(This article belongs to the Special Issue Methyltransferase)
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21 pages, 653 KiB  
Review
Thymic Epithelial Neoplasms: Focusing on the Epigenetic Alterations
by Iason Psilopatis, Alexandros Pergaris, Kleio Vrettou, Stamatios Theocharis and Constantinos Troungos
Int. J. Mol. Sci. 2022, 23(7), 4045; https://doi.org/10.3390/ijms23074045 - 6 Apr 2022
Cited by 11 | Viewed by 3755
Abstract
Thymic Epithelial Neoplasms (TENs) represent the most common tumors of the thymus gland. Epigenetic alterations are generally involved in initiation and progression of various cancer entities. However, little is known about the role of epigenetic modifications in TENs. In order to identify relevant [...] Read more.
Thymic Epithelial Neoplasms (TENs) represent the most common tumors of the thymus gland. Epigenetic alterations are generally involved in initiation and progression of various cancer entities. However, little is known about the role of epigenetic modifications in TENs. In order to identify relevant studies, a literature review was conducted using the MEDLINE and LIVIVO databases. The search terms thymoma, thymic carcinoma, thymic epithelial neoplasm, epigenetics, DNA methylation, HDAC and miRNA were employed and we were able to identify forty studies focused on TENs and published between 1997 and 2021. Aberrant epigenetic alterations seem to be involved in the tumorigenesis of thymomas and thymic carcinomas, with numerous studies reporting on non-coding RNA clusters and altered gene methylation as possible biomarkers in different types of TENs. Interestingly, Histone Deacetylase Inhibitors have shown potent antitumor effects in clinical trials, thus possibly representing effective epigenetic therapeutic agents in TENs. Additional studies in larger patient cohorts are, nevertheless, needed to verify the clinical utility and safety of novel epigenetic agents in the treatment of patients with TENs. Full article
(This article belongs to the Special Issue Molecular Advances in Cancer Therapy)
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14 pages, 2569 KiB  
Review
Stromal Factors as a Target for Immunotherapy in Melanoma and Non-Melanoma Skin Cancers
by Taku Fujimura
Int. J. Mol. Sci. 2022, 23(7), 4044; https://doi.org/10.3390/ijms23074044 - 6 Apr 2022
Cited by 11 | Viewed by 3274
Abstract
Immune checkpoint inhibitors (ICIs), such as anti-programmed cell death 1 (PD1) antibodies (Abs) and anti-cytotoxic T-lymphocyte associated protein 4 (CTLA4) Abs, have been widely administered for not only advanced melanoma, but also various non-melanoma skin cancers. Since profiles of tumor-infiltrating leukocytes (TILs) play [...] Read more.
Immune checkpoint inhibitors (ICIs), such as anti-programmed cell death 1 (PD1) antibodies (Abs) and anti-cytotoxic T-lymphocyte associated protein 4 (CTLA4) Abs, have been widely administered for not only advanced melanoma, but also various non-melanoma skin cancers. Since profiles of tumor-infiltrating leukocytes (TILs) play important roles in immunotherapy using ICIs, it is important to evaluate cancer stromal cells such as tumor-associated macrophages (TAMs) and cancer-associated fibroblasts (CAFs), as well as stromal extracellular matrix protein, to predict the efficacy of ICIs. This review article focuses particularly on TAMs and related factors. Among TILs, TAMs and their related factors could be the optimal biomarkers for immunotherapy such as anti-PD1 Ab therapy. According to the studies presented, TAM-targeting therapies for advanced melanoma and non-melanoma skin cancer will develop in the future. Full article
(This article belongs to the Special Issue Immunomodulation of Skin Cancer)
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16 pages, 2021 KiB  
Review
Emerging Roles of Motile Epidermal Chloroplasts in Plant Immunity
by Hiroki Irieda
Int. J. Mol. Sci. 2022, 23(7), 4043; https://doi.org/10.3390/ijms23074043 - 6 Apr 2022
Cited by 5 | Viewed by 3155
Abstract
Plant epidermis contains atypical small chloroplasts. However, the physiological role of this organelle is unclear compared to that of large mesophyll chloroplasts, the well-known function of which is photosynthesis. Although knowledge of the involvement of chloroplasts in the plant immunity has been expanded [...] Read more.
Plant epidermis contains atypical small chloroplasts. However, the physiological role of this organelle is unclear compared to that of large mesophyll chloroplasts, the well-known function of which is photosynthesis. Although knowledge of the involvement of chloroplasts in the plant immunity has been expanded to date, the differences between the epidermal and mesophyll chloroplasts are beyond the scope of this study. Given the role of the plant epidermis as a barrier to environmental stresses, including pathogen attacks, and the immune-related function of chloroplasts, plant defense research on epidermal chloroplasts is an emerging field. Recent studies have revealed the dynamic movements of epidermal chloroplasts in response to fungal and oomycete pathogens. Furthermore, epidermal chloroplast-associated proteins and cellular events that are tightly linked to epidermal resistance against pathogens have been reported. In this review, I have focused on the recent progress in epidermal chloroplast-mediated plant immunity. Full article
(This article belongs to the Special Issue Molecular Plant-Microbe Interactions)
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13 pages, 817 KiB  
Article
Identifying Genetic Biomarkers Predicting Response to Anti-Vascular Endothelial Growth Factor Injections in Diabetic Macular Edema
by Rajya L. Gurung, Liesel M. FitzGerald, Ebony Liu, Bennet J. McComish, Georgia Kaidonis, Bronwyn Ridge, Alex W. Hewitt, Brendan J. Vote, Nitin Verma, Jamie E. Craig and Kathryn P. Burdon
Int. J. Mol. Sci. 2022, 23(7), 4042; https://doi.org/10.3390/ijms23074042 - 6 Apr 2022
Cited by 5 | Viewed by 3632
Abstract
Intraocular anti-vascular endothelial growth factor (VEGF) therapies are the front-line treatment for diabetic macular edema (DME); however, treatment response varies widely. This study aimed to identify genetic determinants associated with anti-VEGF treatment response in DME. We performed a genome-wide association study on 220 [...] Read more.
Intraocular anti-vascular endothelial growth factor (VEGF) therapies are the front-line treatment for diabetic macular edema (DME); however, treatment response varies widely. This study aimed to identify genetic determinants associated with anti-VEGF treatment response in DME. We performed a genome-wide association study on 220 Australian patients with DME treated with anti-VEGF therapy, genotyped on the Illumina Global Screening Array, and imputed to the Haplotype Reference Consortium panel. The primary outcome measures were changes in central macular thickness (CMT in microns) and best-corrected visual acuity (BCVA in ETDRS letters) after 12 months. Association between single nucleotide polymorphism (SNP) genotypes and DME outcomes were evaluated by linear regression, adjusting for the first three principal components, age, baseline CMT/BCVA, duration of diabetic retinopathy, and HbA1c. Two loci reached genome-wide significance (p < 5 × 10−8) for association with increased CMT: a single SNP on chromosome 6 near CASC15 (rs78466540, p = 1.16 × 10−9) and a locus on chromosome 12 near RP11-116D17.1 (top SNP rs11614480, p = 2.69 × 10−8). Four loci were significantly associated with reduction in BCVA: two loci on chromosome 11, downstream of NTM (top SNP rs148980760, p = 5.30 × 10−9) and intronic in RP11-744N12.3 (top SNP rs57801753, p = 1.71 × 10−8); one near PGAM1P1 on chromosome 5 (rs187876551, p = 1.52 × 10−8); and one near TBC1D32 on chromosome 6 (rs118074968, p = 4.94 × 10−8). In silico investigations of each locus identified multiple expression quantitative trait loci and potentially relevant candidate genes warranting further analysis. Thus, we identified multiple genetic loci predicting treatment outcomes for anti-VEGF therapies in DME. This work may potentially lead to managing DME using personalized treatment approaches. Full article
(This article belongs to the Special Issue Precision Medicine in Retinal Diseases)
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34 pages, 3467 KiB  
Review
In Mitosis You Are Not: The NIMA Family of Kinases in Aspergillus, Yeast, and Mammals
by Scott Bachus, Drayson Graves, Lauren Fulham, Nikolas Akkerman, Caelan Stephanson, Jessica Shieh and Peter Pelka
Int. J. Mol. Sci. 2022, 23(7), 4041; https://doi.org/10.3390/ijms23074041 - 6 Apr 2022
Cited by 6 | Viewed by 4125
Abstract
The Never in mitosis gene A (NIMA) family of serine/threonine kinases is a diverse group of protein kinases implicated in a wide variety of cellular processes, including cilia regulation, microtubule dynamics, mitotic processes, cell growth, and DNA damage response. The founding member of [...] Read more.
The Never in mitosis gene A (NIMA) family of serine/threonine kinases is a diverse group of protein kinases implicated in a wide variety of cellular processes, including cilia regulation, microtubule dynamics, mitotic processes, cell growth, and DNA damage response. The founding member of this family was initially identified in Aspergillus and was found to play important roles in mitosis and cell division. The yeast family has one member each, Fin1p in fission yeast and Kin3p in budding yeast, also with functions in mitotic processes, but, overall, these are poorly studied kinases. The mammalian family, the main focus of this review, consists of 11 members named Nek1 to Nek11. With the exception of a few members, the functions of the mammalian Neks are poorly understood but appear to be quite diverse. Like the prototypical NIMA, many members appear to play important roles in mitosis and meiosis, but their functions in the cell go well beyond these well-established activities. In this review, we explore the roles of fungal and mammalian NIMA kinases and highlight the most recent findings in the field. Full article
(This article belongs to the Special Issue Genome Instability in Health and Disease)
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4 pages, 188 KiB  
Editorial
Molecular Aspects of Renal Immunology: Current Status and Future Perspectives
by Theodoros Eleftheriadis and Marta Crespo
Int. J. Mol. Sci. 2022, 23(7), 4040; https://doi.org/10.3390/ijms23074040 - 6 Apr 2022
Cited by 1 | Viewed by 1651
Abstract
Kidney transplantation is the most promising treatment available for patients with end-stage kidney disease [...] Full article
(This article belongs to the Special Issue Molecular Aspects of Renal Immunology: Current Status and Future Perspectives)
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