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24 pages, 3809 KiB  
Article
The Proteasome and Cul3-Dependent Protein Ubiquitination Is Required for Gli Protein-Mediated Activation of Gene Expression in the Hedgehog Pathway
by Tomasz Uśpieński and Paweł Niewiadomski
Cells 2024, 13(17), 1496; https://doi.org/10.3390/cells13171496 - 6 Sep 2024
Viewed by 1674
Abstract
Many cellular processes are regulated by proteasome-mediated protein degradation, including regulation of signaling pathways and gene expression. Among the pathways regulated by the ubiquitin–proteasome system is the Hedgehog pathway and its downstream effectors, the Gli transcription factors. Here we provide evidence that proteasomal [...] Read more.
Many cellular processes are regulated by proteasome-mediated protein degradation, including regulation of signaling pathways and gene expression. Among the pathways regulated by the ubiquitin–proteasome system is the Hedgehog pathway and its downstream effectors, the Gli transcription factors. Here we provide evidence that proteasomal activity is necessary for maintaining the activation of the Hedgehog pathway, and this crucial event takes place at the level of Gli proteins. We undertook extensive work to demonstrate the specificity of the observed phenomenon by ruling out the involvement of primary cilium, impaired nuclear import, failed dissociation from Sufu, microtubule stabilization, and stabilization of Gli repressor forms. Moreover, we showed that proteasomal-inhibition-mediated Hedgehog pathway downregulation is not restricted to the NIH-3T3 cell line. We demonstrated, using CRISPR/Ca9 mutagenesis, that neither Gli1, Gli2, nor Gli3 are solely responsible for the Hedgehog pathway downregulation upon proteasome inhibitor treatment, and that Cul3 KO renders the same phenotype. Finally, we report two novel E3 ubiquitin ligases, Btbd9 and Kctd3, known Cul3 interactors, as positive Hedgehog pathway regulators. Our data pave the way for a better understanding of the regulation of gene expression and the Hedgehog signaling pathway. Full article
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16 pages, 2771 KiB  
Article
Machine Learning Gene Signature to Metastatic ccRCC Based on ceRNA Network
by Epitácio Farias, Patrick Terrematte and Beatriz Stransky
Int. J. Mol. Sci. 2024, 25(8), 4214; https://doi.org/10.3390/ijms25084214 - 11 Apr 2024
Cited by 2 | Viewed by 2467
Abstract
Clear-cell renal-cell carcinoma (ccRCC) is a silent-development pathology with a high rate of metastasis in patients. The activity of coding genes in metastatic progression is well known. New studies evaluate the association with non-coding genes, such as competitive endogenous RNA (ceRNA). This study [...] Read more.
Clear-cell renal-cell carcinoma (ccRCC) is a silent-development pathology with a high rate of metastasis in patients. The activity of coding genes in metastatic progression is well known. New studies evaluate the association with non-coding genes, such as competitive endogenous RNA (ceRNA). This study aims to build a ceRNA network and a gene signature for ccRCC associated with metastatic development and analyze their biological functions. Using data from The Cancer Genome Atlas (TCGA), we constructed the ceRNA network with differentially expressed genes, assembled nine preliminary gene signatures from eight feature selection techniques, and evaluated the classification metrics to choose a final signature. After that, we performed a genomic analysis, a risk analysis, and a functional annotation analysis. We present an 11-gene signature: SNHG15, AF117829.1, hsa-miR-130a-3p, hsa-mir-381-3p, BTBD11, INSR, HECW2, RFLNB, PTTG1, HMMR, and RASD1. It was possible to assess the generalization of the signature using an external dataset from the International Cancer Genome Consortium (ICGC-RECA), which showed an Area Under the Curve of 81.5%. The genomic analysis identified the signature participants on chromosomes with highly mutated regions. The hsa-miR-130a-3p, AF117829.1, hsa-miR-381-3p, and PTTG1 were significantly related to the patient’s survival and metastatic development. Additionally, functional annotation resulted in relevant pathways for tumor development and cell cycle control, such as RNA polymerase II transcription regulation and cell control. The gene signature analysis within the ceRNA network, with literature evidence, suggests that the lncRNAs act as “sponges” upon the microRNAs (miRNAs). Therefore, this gene signature presents coding and non-coding genes and could act as potential biomarkers for a better understanding of ccRCC. Full article
(This article belongs to the Special Issue Machine Learning and Bioinformatics in Human Health and Disease)
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19 pages, 14989 KiB  
Article
MiR-202-5p Regulates Geese Follicular Selection by Targeting BTBD10 to Regulate Granulosa Cell Proliferation and Apoptosis
by Mingxia Ran, Shenqiang Hu, Hengli Xie, Qingyuan Ouyang, Xi Zhang, Yueyue Lin, Xin Yuan, Jiwei Hu, Hua He, Hehe Liu, Liang Li and Jiwen Wang
Int. J. Mol. Sci. 2023, 24(7), 6792; https://doi.org/10.3390/ijms24076792 - 5 Apr 2023
Cited by 10 | Viewed by 2112
Abstract
The regulation of granulosa cells (GCs) proliferation and apoptosis is the key step in follicular selection which determines the egg production performance of poultry. miR-202-5p has been reported to be involved in regulating the proliferation and apoptosis of mammalian ovarian GCs. However, its [...] Read more.
The regulation of granulosa cells (GCs) proliferation and apoptosis is the key step in follicular selection which determines the egg production performance of poultry. miR-202-5p has been reported to be involved in regulating the proliferation and apoptosis of mammalian ovarian GCs. However, its role in regulating the proliferation and apoptosis of goose GCs is still unknown. In the present study, the GCs of pre-hierarchical follicles (phGCs, 8–10 mm) and those of hierarchical follicles (hGCs, F2–F4) were used to investigate the role of miR-202-5p in cell proliferation and apoptosis during follicle selection. In phGCs and hGCs cultured in vitro, miR-202-5p was found to negatively regulate cell proliferation and positively regulate cell apoptosis. The results of RNA-seq showed that BTB Domain Containing 10 (BTBD10) is predicted to be a key target gene for miR-202-5p to regulate the proliferation and apoptosis of GCs. Furthermore, it is confirmed that miR-202-5p can inhibit BTBD10 expression by targeting its 3′UTR region, and BTBD10 was revealed to promote the proliferation and inhibit the apoptosis of phGCs and hGCs. Additionally, co-transfection with BTBD10 effectively prevented miR-202-5p mimic-induced cell apoptosis and the inhibition of cell proliferation. Meanwhile, miR-202-5p also remarkably inhibited the expression of Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit Beta (PIK3CB) and AKT Serine/Threonine Kinase 1 (AKT1), while it was significantly restored by BTBD10. Overall, miR-202-5p suppresses the proliferation and promotes the apoptosis of GCs through the downregulation of PIK3CB/AKT1 signaling by targeting BTBD10 during follicular selection. Our study provides a theoretical reference for understanding the molecular mechanism of goose follicular selection, as well as a candidate gene for molecular marker-assisted breeding to improve the geese’ egg production performance. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
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15 pages, 434 KiB  
Review
The Aetiology of Tourette Syndrome and Chronic Tic Disorder in Children and Adolescents: A Comprehensive Systematic Review of Case-Control Studies
by Jilong Jiang, Mengxin Chen, Huifang Huang and Yanhui Chen
Brain Sci. 2022, 12(9), 1202; https://doi.org/10.3390/brainsci12091202 - 6 Sep 2022
Cited by 6 | Viewed by 3291
Abstract
(1) Introduction: Tourette syndrome (TS) and chronic tic disorder (CTD) are common neurodevelopmental/-psychiatric disorders. The aetiological factors that contribute to the pathogenesis of TS/CTD are still poorly understood. The possible risk factors for TS/CTD are considered to be a combination of genetic, immunological, [...] Read more.
(1) Introduction: Tourette syndrome (TS) and chronic tic disorder (CTD) are common neurodevelopmental/-psychiatric disorders. The aetiological factors that contribute to the pathogenesis of TS/CTD are still poorly understood. The possible risk factors for TS/CTD are considered to be a combination of genetic, immunological, psychological and environmental factors. A comprehensive systematic review was conducted to assess the association between aetiological factors and TS/CTD. (2) Methods: Electronic databases, including PubMed, Embase, Web of Science, Wanfang data, and CNKI, were searched to identify the etiological factors of children and adolescents (≤18 years) with TS/CTD based on a case-control study. Quality assessments were performed according to the Newcastle-Ottawa scale (NOS). (3) Results: According to sample sizes and NOS values, recent evidence may support that genetic factors (BTBD9 and AADAC), immunological factors (streptococcus and mycoplasma pneumoniae infections), environmental factors (conflict, history of perinatal diseases, and family history of neurological and psychiatric diseases and recurrent respiratory infections) and psychological factors (major life events) are associated with the pathogenesis of TS/CTD. (4) Conclusions: Some risk factors in different categories may be the etiological factors of TS/CTD, but there is a lack of studies on the interaction among the factors, which may require more attention in the future. Full article
(This article belongs to the Special Issue New Insights in Neurobiology and Genetics of Tourette Syndrome)
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20 pages, 3946 KiB  
Article
Artificial-Intelligence-Assisted Discovery of Genetic Factors for Precision Medicine of Antiplatelet Therapy in Diabetic Peripheral Artery Disease
by Chi-Hsiao Yeh, Yi-Ju Chou, Tsung-Hsien Tsai, Paul Wei-Che Hsu, Chun-Hsien Li, Yun-Hsuan Chan, Shih-Feng Tsai, Soh-Ching Ng, Kuei-Mei Chou, Yu-Ching Lin, Yu-Hsiang Juan, Tieh-Cheng Fu, Chi-Chun Lai, Huey-Kang Sytwu and Ting-Fen Tsai
Biomedicines 2022, 10(1), 116; https://doi.org/10.3390/biomedicines10010116 - 6 Jan 2022
Cited by 12 | Viewed by 3972
Abstract
An increased risk of cardiovascular events was identified in patients with peripheral artery disease (PAD). Clopidogrel is one of the most widely used antiplatelet medications. However, there are heterogeneous outcomes when clopidogrel is used to prevent cardiovascular events in PAD patients. Here, we [...] Read more.
An increased risk of cardiovascular events was identified in patients with peripheral artery disease (PAD). Clopidogrel is one of the most widely used antiplatelet medications. However, there are heterogeneous outcomes when clopidogrel is used to prevent cardiovascular events in PAD patients. Here, we use an artificial intelligence (AI)-assisted methodology to identify genetic factors potentially involved in the clopidogrel-resistant mechanism, which is currently unclear. Several discoveries can be pinpointed. Firstly, a high proportion (>50%) of clopidogrel resistance was found among diabetic PAD patients in Taiwan. Interestingly, our result suggests that platelet function test-guided antiplatelet therapy appears to reduce the post-interventional occurrence of major adverse cerebrovascular and cardiac events in diabetic PAD patients. Secondly, AI-assisted genome-wide association study of a single-nucleotide polymorphism (SNP) database identified a SNP signature composed of 20 SNPs, which are mapped into 9 protein-coding genes (SLC37A2, IQSEC1, WASHC3, PSD3, BTBD7, GLIS3, PRDM11, LRBA1, and CNR1). Finally, analysis of the protein connectivity map revealed that LRBA, GLIS3, BTBD7, IQSEC1, and PSD3 appear to form a protein interaction network. Intriguingly, the genetic factors seem to pinpoint a pathway related to endocytosis and recycling of P2Y12 receptor, which is the drug target of clopidogrel. Our findings reveal that a combination of AI-assisted discovery of SNP signatures and clinical parameters has the potential to develop an ethnic-specific precision medicine for antiplatelet therapy in diabetic PAD patients. Full article
(This article belongs to the Special Issue Cardiovascular Medicine: From Bench to Bedside)
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10 pages, 1413 KiB  
Article
Genetic Dissection of Temperament Personality Traits in Italian Isolates
by Maria Pina Concas, Alessandra Minelli, Susanna Aere, Anna Morgan, Paola Tesolin, Paolo Gasparini, Massimo Gennarelli and Giorgia Girotto
Genes 2022, 13(1), 4; https://doi.org/10.3390/genes13010004 - 21 Dec 2021
Cited by 3 | Viewed by 5609
Abstract
Human personality (i.e., temperament and character) is a complex trait related to mental health, influenced by genetic and environmental factors. Despite the efforts performed during the past decades, its genetic background is only just beginning to be identified. With the aim of dissecting [...] Read more.
Human personality (i.e., temperament and character) is a complex trait related to mental health, influenced by genetic and environmental factors. Despite the efforts performed during the past decades, its genetic background is only just beginning to be identified. With the aim of dissecting the genetic basis of temperament, we performed a Genome-Wide Association Study (GWAS) on Cloninger’s Temperament and Character Inventory in 587 individuals belonging to different Italian genetic isolates. Data analysis led to the identification of four new genes associated with different temperament scales, such as Novelty Seeking (NS), Harm Avoidance (HA), and Reward Dependence (RD). In detail, we identified suggestive and significant associations between: MAGI2 (highest p-value = 9.14 × 10−8), a gene already associated with schizophrenia and depressive disorder, and the NS–Extravagance scale; CALCB (highest p-value = 4.34 × 10−6), a gene likely involved in the behavioral evolution from wild wolf to domestic dog, and the NS–Disorderliness scale; BTBD3 (highest p-value = 2.152 × 10−8), a gene already linked to obsessive–compulsive disorder, and the HA–Fatigability scale; PRKN (highest p-value = 8.27 × 10−9), a gene described for early onset Parkinson’s disease, and the RD scale. Our work provides new relevant insights into the genetics of temperament, helping to elucidate the molecular basis of psychiatric disorders. Full article
(This article belongs to the Special Issue Genetics of Psychiatric Disease and the Basics of Neurobiology)
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20 pages, 5039 KiB  
Article
circBTBD7 Promotes Immature Porcine Sertoli Cell Growth through Modulating miR-24-3p/MAPK7 Axis to Inactivate p38 MAPK Signaling Pathway
by Qiao Bian, Bin Chen, Bo Weng, Dan Chu, Xiangwei Tang, Saina Yan, Yanfei Yin and Maoliang Ran
Int. J. Mol. Sci. 2021, 22(17), 9385; https://doi.org/10.3390/ijms22179385 - 30 Aug 2021
Cited by 13 | Viewed by 2847
Abstract
Sertoli cells are the crucial coordinators to guarantee normal spermatogenesis and male fertility. Although circular RNAs (circRNAs) exhibit developmental-stage-specific expression in porcine testicular tissues and have been thought of as potential regulatory molecules in spermatogenesis, their functions and mechanisms of action remain largely [...] Read more.
Sertoli cells are the crucial coordinators to guarantee normal spermatogenesis and male fertility. Although circular RNAs (circRNAs) exhibit developmental-stage-specific expression in porcine testicular tissues and have been thought of as potential regulatory molecules in spermatogenesis, their functions and mechanisms of action remain largely unknown, especially in domestic animals. A novel circBTBD7 was identified from immature porcine Sertoli cells using reverse transcription PCR, Sanger sequencing, and fluorescence in situ hybridization assays. Functional assays illustrated that circBTBD7 overexpression promoted cell cycle progression and cell proliferation, as well as inhibited cell apoptosis in immature porcine Sertoli cells. Mechanistically, circBTBD7 acted as a sponge for the miR-24-3p and further facilitated its target mitogen-activated protein kinase 7 (MAPK7) gene. Overexpression of miR-24-3p impeded cell proliferation and induced cell apoptosis, which further attenuated the effects of circBTBD7 overexpression. siRNA-induced MAPK7 deficiency resulted in a similar effect to miR-24-3p overexpression, and further offset the effects of miR-24-3p inhibition. Both miR-24-3p overexpression and MAPK7 knockdown upregulated the p38 phosphorylation activity. The SB202190 induced the inhibition of p38 MAPK pathway and caused an opposite effect to that of miR-24-3p overexpression and MAPK7 knockdown. Collectively, circBTBD7 promotes immature porcine Sertoli cell growth through modulating the miR-24-3p/MAPK7 axis to inactivate the p38 MAPK signaling pathway. This study expanded our knowledge of noncoding RNAs in porcine normal spermatogenesis through deciding the fate of Sertoli cells. Full article
(This article belongs to the Section Biochemistry)
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11 pages, 2201 KiB  
Review
Genetic Variations Associated with Sleep Disorders in Patients with Schizophrenia: A Systematic Review
by Konstantinos Assimakopoulos, Katerina Karaivazoglou, Maria Skokou, Marina Kalogeropoulou, Panagiotis Kolios, Philippos Gourzis, George P. Patrinos and Evangelia Eirini Tsermpini
Medicines 2018, 5(2), 27; https://doi.org/10.3390/medicines5020027 - 24 Mar 2018
Cited by 10 | Viewed by 6880
Abstract
Background: Schizophrenic patients commonly suffer from sleep disorders which are associated with acute disease severity, worsening prognoses and a poorer quality of life. Research is attempting to disentangle the complex interplay between schizophrenia and sleep disturbances by focusing not only on demographic and [...] Read more.
Background: Schizophrenic patients commonly suffer from sleep disorders which are associated with acute disease severity, worsening prognoses and a poorer quality of life. Research is attempting to disentangle the complex interplay between schizophrenia and sleep disturbances by focusing not only on demographic and clinical characteristics, but also on the identification of genetic factors. Methods: Here, we performed a systematic literature review on the topic of genetic variations in sleep-disordered schizophrenic patients in an attempt to identify high quality investigations reporting scientifically sound and clinically useful data. For this purpose, we conducted a thorough search of PubMed, ScienceDirect and GoogleScholar databases, according to the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-analysis (PRISMA) protocol. Results: Our search yielded 11 eligible studies. Certain genetic variations were reported to be associated with schizophrenia-related sleep disorders. Antipsychotic-induced restless legs syndrome was linked to polymorphisms located on CLOCK, BTBD9, GNB3, and TH genes, clozapine-induced somnolence was correlated with polymorphisms of HNMT gene, while insomnia was associated with variants of the MTNR1 gene. Conclusions: There are significant genetic associations between schizophrenia and co-morbid sleep disorders, implicating the circadian system, dopamine and histamine metabolism and signal transduction pathways. Full article
(This article belongs to the Special Issue Schizophrenia and Sleep Disorders)
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