Ubiquitin‐conjugating enzyme E2T (UBE2T) has been implicated in many types of cancer including hepatocellular carcinoma (HCC). Epithelial–mesenchymal transition (EMT) process plays a fundamental role ...during tumor metastasis and progression. However, the molecular mechanisms underlying EMT in HCC in accordance with UBE2T still remain unknown. In this study, we showed that UBE2T overexpression augmented the oncogenic properties and specifically EMT in HCC cell lines, while its silencing attenuated them. UBE2T affected the activation of EMT‐associated signaling pathways: MAPK/ERK, AKT/mTOR, and Wnt/β‐catenin. In addition, we revealed that the epithelial protein complex of E‐cadherin/β‐catenin, a vital regulator of signal transduction in tumor initiation and progression, was totally disrupted at the cell membrane. In particular, we observed that UBE2T overexpression led to E‐cadherin loss accompanied by a simultaneous elevation of both cytoplasmic and nuclear β‐catenin, while its silencing resulted in a strong E‐cadherin turnover at the cell membrane. Interestingly, chemical inhibition of the MAPK/ERK, AKT/mTOR, and Wnt/β‐catenin signaling pathways demonstrated that the nuclear translocation of β‐catenin and subsequent EMT was enhanced mainly by MAPK/ERK. Collectively, our findings demonstrate the UBE2T/MAPK‐ERK/β‐catenin axis as a critical regulator of cell state transition and EMT in HCC.
Hepatocellular carcinoma (HCC) is the third leading cause of cancer deaths worldwide. In this study, the authors investigated the role of ubiquitin‐conjugating enzyme E2T (UBE2T) in epithelial–mesenchymal transition (EMT) in HCC. UBE2T promoted EMT via E‐cadherin/β‐catenin disruption at the cell membrane and β‐catenin nuclear translocation through MAPK‐ERK‐dependent activation. Therefore, the UBE2T/MAPK‐ERK/β‐catenin axis may serve as a promising target for HCC treatment.
Excessive growth of terminal hair around the elbows (hypertrichosis cubiti) has been reported both in isolation and in association with a variable spectrum of associated phenotypic features. We ...identified a cohort of six individuals with hypertrichosis cubiti associated with short stature, intellectual disability, and a distinctive facial appearance, consistent with a diagnosis of Wiedemann-Steiner syndrome (WSS). Utilizing a whole-exome sequencing approach, we identified de novo mutations in MLL in five of the six individuals. MLL encodes a histone methyltransferase that regulates chromatin-mediated transcription through the catalysis of methylation of histone H3K4. Each of the five mutations is predicted to result in premature termination of the protein product. Furthermore, we demonstrate that transcripts arising from the mutant alleles are subject to nonsense-mediated decay. These findings define the genetic basis of WSS, provide additional evidence for the role of haploinsufficency of histone-modification enzymes in multiple-congenital-anomaly syndromes, and further illustrate the importance of the regulation of histone modification in development.
Amyotrophic lateral sclerosis (ALS) is a rare progressive neurodegenerative disease that affects upper and lower motor neurons. As the molecular basis of the disease is still elusive, the development ...of high-throughput sequencing technologies, combined with data mining techniques and machine learning methods, could provide remarkable results in identifying pathogenetic mechanisms. High dimensionality is a major problem when applying machine learning techniques in biomedical data analysis, since a huge number of features is available for a limited number of samples. The aim of this study was to develop a methodology for training interpretable machine learning models in the classification of ALS and ALS-subtypes samples, using gene expression datasets.
We performed dimensionality reduction in gene expression data using a semi-automated preprocessing systematic gene selection procedure using Statistically Equivalent Signature (SES), a causality-based feature selection algorithm, followed by Boosted Regression Trees (XGBoost) and Random Forest to train the machine learning classifiers. The SHapley Additive exPlanations (SHAP values) were used for interpretation of the machine learning classifiers. The methodology was developed and tested using two distinct publicly available ALS RNA-seq datasets. We evaluated the performance of SES as a dimensionality reduction method against: (a) Least Absolute Shrinkage and Selection Operator (LASSO), and (b) Local Outlier Factor (LOF).
The proposed methodology achieved 85.18% accuracy for the classification of cerebellum or frontal cortex samples as C9orf72-related familial ALS, sporadic ALS or healthy samples. Importantly, the genes identified as the most determinative have also been reported as disease-associated in ALS literature. When tested in the evaluation dataset, the methodology achieved 88.89% accuracy for the classification of sporadic ALS motor neuron samples. When LASSO was used as feature selection method instead of SES, the accuracy of the machine learning classifiers ranged from 74.07 to 96.30%, depending on tissue assessed, while LOF underperformed significantly (77.78% accuracy for the classification of pooled cerebellum and frontal cortex samples).
Using SES, we addressed the challenge of high dimensionality in gene expression data analysis, and we trained accurate machine learning ALS classifiers, specific for the gene expression patterns of different disease subtypes and tissue samples, while identifying disease-associated genes.
Progressive matrix metalloproteinase (MMP)-induced degradation of the extracellular matrix (ECM) of the articular cartilage is one of the major pathogenic osteoarthritis (OA) events. Several single ...nucleotide polymorphisms (SNPs) in genes encoding MMPs have been identified as affecting MMP expression, production, and enzymatic activity. This study systematically reviews the literature regarding the association between the SNPs of genes encoding MMPs and the risk of knee OA. An electronic search in the PubMed and Web of Science databases from conception to January 2021 was performed addressing studies relating MMPs genetic polymorphisms with the risk of knee OA. We included case-control studies that used validated genotyping methods to detect the SNPs’ association in MMP genes with primary knee OA risk. Ten studies were finally included in this systematic review, evaluating different SNPs in six MMP genes in terms of knee OA pathogenesis: MMP-1 (3 SNPs), MMP-2 (1 SNP), MMP-3 (9 SNPs), MMP-8 (10 SNPs), MMP-9 (6 SNPs), and MMP-13 (1 SNP). Among them, nine SNPs of four MMP genes have been associated with knee OA: (a) MMP-1 -1607 1G/2G (Turkish, Chinese), (b) MMP-3 rs650108, rs650108, rs520540, rs602128, rs679620 (Chinese), (c) MMP-8 rs1940475 and rs376520 (Finnish), and (d) MMP-13 77A/ (rs2252070) (Chinese). The present review summarizes all known SNPs of MMP genes related to a higher risk of knee OA. There are at least nine SNPs in four MMP genes associated with knee OA. No solid correlation between MMP genotype and knee OA phenotype exists. More high-quality studies and modern genetic testing methods are needed to fully elucidate the role of polymorphisms of MMP genes in knee OA pathogenesis.
Photocatalytic inactivation of pathogens in aqueous waste is gaining increasing attention. Several homogeneous and heterogeneous photocatalytic protocols exist using the Fenton’s reagent and TiO2, ...respectively. A comprehensive study of homogeneous and heterogeneous photocatalysis on a range of microorganisms will significantly establish the most efficient method. Here, we report a comparative study of TiO2- and Fe+3-based photocatalytic inactivation under UV-A of diverse microorganisms, including Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria, bacterial spores (Bacillus stearothermophilus spores) and viruses (MS2). We also present data on the optimization of TiO2 photocatalysis, including optimal catalyst concentration and H2O2 supplementation. Our results indicate that both photo-Fenton and TiO2 could be successfully applied for the management of microbial loads in liquids. Efficient microorganism inactivation is achieved with homogeneous photocatalysis (7 mg/L Fe+3, 100 mg/L H2O2, UV-A) in a shorter processing time compared to heterogeneous photocatalysis (0.5 g/L TiO2, UV-A), whereas similar or shorter processing is required when heterogenous photocatalysis is performed using microorganism-specific optimized TiO2 concentrations and H2O2 supplementation (100 mg/L); higher H2O2 concentrations further enhance the heterogenous photocatalytic inactivation efficiency. Our study provides a template protocol for the design and further application for large-scale photocatalytic approaches to inactivate pathogens in liquid biomedical waste.
CYLD is a tumor suppressor gene coding for a deubiquitinating enzyme that has a critical regulatory function in a variety of signaling pathways and biological processes involved in cancer development ...and progression, many of which are also key modulators of somatic cell reprogramming. Nevertheless, the potential role of CYLD in this process has not been studied. With the dual aim of investigating the involvement of CYLD in reprogramming and developing a better understanding of the intricate regulatory system governing this process, we reprogrammed control (CYLDWT/WT) and CYLD DUB-deficient (CYLDΔ9/Δ9) mouse embryonic fibroblasts (MEFs) into induced pluripotent stem cells (iPSCs) through ectopic overexpression of the Yamanaka factors (Oct3/4, Sox2, Klf4, c-myc). CYLD DUB deficiency led to significantly reduced reprogramming efficiency and slower early reprogramming kinetics. The introduction of WT CYLD to CYLDΔ9/Δ9 MEFs rescued the phenotype. Nevertheless, CYLD DUB-deficient cells were capable of establishing induced pluripotent colonies with full spontaneous differentiation potential of the three germ layers. Whole proteome analysis (Data are available via ProteomeXchange with identifier PXD044220) revealed that the mesenchymal-to-epithelial transition (MET) during the early reprogramming stages was disrupted in CYLDΔ9/Δ9 MEFs. Interestingly, differentially enriched pathways revealed that the primary processes affected by CYLD DUB deficiency were associated with the organization of the extracellular matrix and several metabolic pathways. Our findings not only establish for the first time CYLD’s significance as a regulatory component of early reprogramming but also highlight its role as an extracellular matrix regulator, which has profound implications in cancer research.
Prion diseases, such as the sporadic Creutzfeldt–Jakob disease (sCJD), are a class of fatal neurodegenerative disorders. Currently, there is no efficient treatment or therapy available. Hence, the ...search for molecules that may inhibit the conversion of the cellular prion protein (PrP
C
) into its pathological counterpart PrPScrapie (PrP
Sc
) is of great urgency. Here, we report the generation- and dose-dependent biological action of dense-shell poly(propylene imine) (PPI) glycodendrimers by using scrapie-infected neuroblastoma (ScN2a) cells and the real-time quaking-induced conversion assay (RT-QuIC) for validation of anti-prion efficiencies. Whereas the 2nd and 3rd generation of PPI glycodendrimers exhibited anti-prion conversion efficiency in ScN2a cells validated by RT-QuIC analysis, we observed that the 4th generation of glycodendrimers had shown no significant effect. Translational RT-QuIC studies conducted with human prions derived from sCJD patients indicated an anti-prion conversion effect (not on PrP
Res
degradation) of PPI glycodendrimers against human prions with the highest inhibitory activity of the 4th generation of PPI glycodendrimers towards prion aggregation compared to the 2nd and 3rd generation. In conclusion, our study highlights the potential of PPI glycodendrimers as therapeutic compounds due to their anti-conversion activity on human prions in a PrP
Sc
strain depending manner.
Human Papillomaviruses have been associated with the occurrence of cervical cancer, the fourth most common cancer that affects women globally, while 70% of cases are caused by infection with the ...high-risk types HPV16 and HPV18. The integration of these viruses' oncogenes
and
into the host's genome affects a multitude of cellular functions and alters the expression of molecules. The aim of this study was to investigate how these oncogenes contribute to the expression of immune system control molecules, using cell lines with integrated HPV16 genome, before and after knocking out
viral gene using the CRISPR/Cas9 system, delivered with a lentiviral vector. The molecules studied are the T-cell inactivating protein PD-L1, its transcription factor HIF-1a and the latter's negative regulator, miR-143. According to our results, in the E6 knock out (E6KO) cell lines an increased expression of miR-143 was recorded, while a decrease in the expression of HIF-1a and PD-L1 was exhibited. These findings indicate that E6 protein probably plays a significant role in enabling cervical cancer cells to evade the immune system, while we propose a molecular pathway in cervical cancer, where PD-L1's expression is regulated by E6 protein through a miR-143/HIF-1a axis.
Prion diseases, also known as Transmissible Spongiform Encephalopathies (TSEs), are protein-based neurodegenerative disorders (NDs) affecting humans and animals. They are characterized by the ...conformational conversion of the normal cellular prion protein, PrPC, into the pathogenic isoform, PrPSc. Prion diseases are invariably fatal and despite ongoing research, no effective prophylactic or therapeutic avenues are currently available. Anthocyanins (ACNs) are unique flavonoid compounds and interest in their use as potential neuroprotective and/or therapeutic agents against NDs, has increased significantly in recent years. Therefore, we investigated the potential anti-oxidant and anti-prion effects of Oenin and Myrtillin, two of the most common anthocyanins, using the most accepted in the field overexpressing PrPScin vitro model and a cell free protein aggregation model. Our results, indicate both anthocyanins as strong anti-oxidant compounds, upregulating the expression of genes involved in the anti-oxidant response, and reducing the levels of Reactive Oxygen Species (ROS), produced due to pathogenic prion infection, through the activation of the Keap1-Nrf2 pathway. Importantly, they showcased remarkable anti-prion potential, as they not only caused the clearance of pathogenic PrPSc aggregates, but also completely inhibited the formation of PrPSc fibrils in the Cerebrospinal Fluid (CSF) of patients with Creutzfeldt–Jakob disease (CJD). Therefore, Oenin and Myrtillin possess pleiotropic effects, suggesting their potential use as promising preventive and/or therapeutic agents in prion diseases and possibly in the spectrum of neurodegenerative proteinopathies.
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•Oenin and Myrtillin reduce ROS production in N2a22L cells.•Oenin and Myrtillin activate the Keap1-Nrf2 axis in N2a22L cells.•Oenin and Myrtillin reduce PrPSc accumulation in N2a22L cells.•Oenin and Myrtillin impede de novo PrPSc formation and aggregation.•Oenin and Myrtillin are potent compounds for intervention against prion diseases.
Microglia are macrophages present in the brain that function as the primary and most important source of immune response in the central nervous system (CNS). Regardless of their multitasking role, ...our knowledge regarding their molecular heterogeneity is limited; due to technical restrictions, it is only possible to measure gene expression in cell populations, not individual cells, with the results reflecting average mRNA levels. Therefore, recent scientific approaches have focused on single-cell techniques such as single-cell RNA sequencing (scRNAseq), a powerful technique that enables the delineation of transcriptomic cell-to-cell differences, revealing subpopulations with distinct molecular and functional characteristics. Here, we summarize recent studies that focused on transcriptomic microglial subpopulation clustering and classify them into three distinct groups based on age, spatial distribution, and disease. Additionally, we cross-compare populations from different studies to identify expressional and functional overlaps between them.
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