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Many noncoding RNAs (ncRNAs) have been identified, and many of them play vital roles in various biological processes, including gene expression regulation, epigenetic regulation, transcription, and control. Recently, a few observations revealed that ncRNAs are translated into functional peptides. Moreover, many computational methods have been developed to predict the coding potential of these transcripts, which contributes to a deeper investigation of their functions. However, most of these are used to distinguish ncRNAs and mRNAs. It is important to develop a highly accurate computational tool for identifying the coding potential of ncRNAs, thereby contributing to the discovery of novel peptides. In this Article, we propose a novel BiLSTM And Transformer encoder-based model (nBAT) with intrinsic features encoded for ncRNA coding potential prediction. In nBAT, we introduce a learnable position encoding mechanism to better obtain the embeddings of the ncRNA sequence. Moreover, we extract 43 intrinsic features from different perspectives and encode these features into the Transformer encoder by calculating their distances. Our performance comparisons show that nBAT achieves a superior performance than the state-of-the-art methods for coding potential prediction on different datasets. We also apply the method to new ncRNAs for identifying the coding potential, and the results further indicate the competitive performance of nBAT. We expect the method can be exploited as a useful tool for high-throughput coding potential prediction for ncRNAs.
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Biologia Computacional , RNA não Traduzido , RNA não Traduzido/genética , Biologia Computacional/métodos , HumanosRESUMO
ATG10S is a newly discovered subtype of the autophagy protein ATG10. It promotes complete macroautophagy/autophagy, degrades multiple viral proteins, and increases the expression of type III interferons. Here, we aimed to investigate the mechanism of ATG10S cooperation with IFNL1 to degrade viral proteins from different viruses. Using western blot, immunoprecipitation (IP), tandem sensor RFP-GFP-LC3B and in situ proximity ligation assays, we showed that exogenous recombinant ATG10S protein (rHsATG10S) could enter into cells through clathrin, and ATG10S combined with ATG7 with IFNL1 assistance to facilitate ATG12-ATG5 conjugation, thereby contributing to the autophagosome formation in multiple cell lines containing different virions or viral proteins. The results of DNA IP and luciferase assays also showed that ATG10S was able to directly bind to a core motif (CAAGGG) within a binding site of transcription factor ZNF460 on the IFNL1 promoter, by which IFNL1 transcription was activated. These results clarified that ATG10S promoted autophagosome formation with the assistance of IFNL1 to ensure autophagy flux and autophagic degradation of multiple viral proteins and that ATG10S could also act as a novel transcription factor to promote IFNL1 gene expression. Importantly, this study further explored the antiviral mechanism of ATG10S interaction with type III interferon and provided a theoretical basis for the development of ATG10S into a new broad-spectrum antiviral protein drug.Abbreviation: ATG: autophagy related; ATG10S: the shorter isoform of autophagy-related 10; CC50: half cytotoxicity concentration; CCV: clathrin-coated transport vesicle; CLTC: clathrin heavy chain; CM: core motif; co-IP: co-immunoprecipitation; CPZ: chlorpromazine; ER: endoplasmic reticulum; HCV: hepatitis C virus; HBV: hepatitis B virus; HsCoV-OC43: Human coronavirus OC43; IFN: interferon; PLA: proximity ligation assay; rHsATG10S: recombinant human ATG10S protein; RLU: relative light unit; SQSTM1: sequestosome 1; ZNF: zinc finger protein.
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Intracerebral hemorrhage (ICH), for which there are currently no effective preventive or treatment methods, has a very high fatality rate. Statins, such as atorvastatin (ATV), are the first-line drugs for regulating blood lipids and treating hyperlipidemia-related cardiovascular diseases. However, ATV-associated ICH has been reported, although its incidence is rare. In this study, we aimed to investigate the protective action and mechanisms of berberine (BBR) against ATV-induced brain hemorrhage. We established an ICH model in zebrafish induced by ATV (2 µM) and demonstrated the effects of BBR (10, 50, and 100 µM) on ICH via protecting the vascular network using hemocyte staining and three transgenic zebrafish. BBR was found to reduce brain inflammation and locomotion injury in ICH-zebrafish. Mechanism research showed that ATV increased the levels of VE-cadherin and occludin proteins but disturbed their localization at the cell membrane by abnormal phosphorylation, which decreased the number of intercellular junctions between vascular endothelial cells (VECs), disrupting the integrity of vascular walls. BBR reversed the effects of ATV by promoting autophagic degradation of phosphorylated VE-cadherin and occludin in ATV-induced VECs examined by co-immunoprecipitation (co-IP). These findings provide crucial insights into understanding the BBR mechanisms involved in the maintenance of vascular integrity and in mitigating adverse reactions to ATV.
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Atorvastatina , Berberina , Hemorragia Cerebral , Peixe-Zebra , Animais , Atorvastatina/farmacologia , Hemorragia Cerebral/induzido quimicamente , Berberina/farmacologia , Animais Geneticamente Modificados , Modelos Animais de Doenças , Células Endoteliais/efeitos dos fármacosRESUMO
BACKGROUND: L-Tryptophan (L-Trp), an essential amino acid, is the only amino acid whose level is regulated specifically by immune signals. Most proportions of Trp are catabolized via the kynurenine (Kyn) pathway (KP) which has evolved to align the food availability and environmental stimulation with the host pathophysiology and behavior. Especially, the KP plays an indispensable role in balancing the immune activation and tolerance in response to pathogens. SCOPE OF REVIEW: In this review, we elucidate the underlying immunological regulatory network of Trp and its KP-dependent catabolites in the pathophysiological conditions by participating in multiple signaling pathways. Furthermore, the KP-based regulatory roles, biomarkers, and therapeutic strategies in pathologically immune disorders are summarized covering from acute to chronic infection and inflammation. MAJOR CONCLUSIONS: The immunosuppressive effects dominate the functions of KP induced-Trp depletion and KP-produced metabolites during infection and inflammation. However, the extending minor branches from the KP are not confined to the immune tolerance, instead they go forward to various functions according to the specific condition. Nevertheless, persistent efforts should be made before the clinical use of KP-based strategies to monitor and cure infectious and inflammatory diseases.
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Biomarcadores , Inflamação , Cinurenina , Triptofano , Triptofano/metabolismo , Cinurenina/metabolismo , Humanos , Inflamação/metabolismo , Inflamação/imunologia , Animais , Biomarcadores/metabolismo , Infecções/imunologia , Infecções/metabolismoRESUMO
Dengue virus (DENV) infection causes dengue fever, the most prevalent arthropod-transmitted viral disease worldwide. Viruses are acellular parasites and obligately rely on host cell machinery for reproduction. Previous studies have indicated metabolomic changes in endothelial cell models and sera of animal models and patients with dengue fever. To probe the immunometabolic mechanism of DENV infection, here, we report the metabolomic landscape of a human macrophage cell model of DENV infection and its antibody-dependent enhancement. DENV infection of THP-1-derived macrophages caused 202 metabolic variants, of which amino acids occupied 23.7%, fatty acids 21.78%, carbohydrates 10.4%, organic acids 13.37%, and carnitines 10.4%. These metabolomic changes indicated an overall anabolic signature, which was characterized by the global exhaustion of amino acids, increases of cellular fatty acids, carbohydrates and pentoses, but decreases of acylcarnitine. Significant activation of metabolic pathways of glycolysis, pentose phosphate, amino acid metabolism, and tricarboxylic acid cycle collectively support the overall anabolism to meet metabolic demands of DENV replication and immune activation by viral infection. Totally 88 of 202 metabolic variants were significantly changed by DENV infection, 36 of which met the statistical standard (P<0.05, VIP>1.5) of differentially expressed metabolites, which were the predominantly decreased variants of acylcarnitine and the increased variants of fatty acids and carbohydrates. Remarkably, 11 differentially expressed metabolites were significantly distinct between DENV only infection and antibody-dependent enhancement of viral infection. Our data suggested that the anabolic activation by DENV infection integrates the viral replication and anti-viral immune activation.
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Carnitina/análogos & derivados , Vírus da Dengue , Dengue , Viroses , Animais , Humanos , Vírus da Dengue/fisiologia , Anticorpos Facilitadores , Replicação Viral , Macrófagos , Carboidratos , Aminoácidos , Ácidos GraxosRESUMO
Recently, beta-lactam antibiotics have gained attention as significant contributors to public health and environmental issues due to their potential toxicity. Our study employed machine learning to develop a model for assessing the aquatic toxicity of beta-lactam antibiotics on zebrafish. Notably, aztreonam (AZT), a synthetic monobactam and a subclass of beta-lactam antibiotics, demonstrated developmental effects in zebrafish embryos comparable to cephalosporins, indicating a potential for toxicity. Using a systems toxicology-based approach, we identified apoptosis and metabolic disorders as the primary pathways affected by AZT and its impurity F exposure. During the administration of monobactams, we noted that ctsbb, nos2a, and dgat2, genes associated with apoptosis and the metabolic pathway, exhibited significant differential expression. Molecular docking studies were conducted to ascertain the binding affinity between monobactam compounds and their potential targets-Ctsbb, Nos2a, and Dgat2. Furthermore, our research revealed that monobactams influence pre-mRNA alternative splicing, resulting in disruptions in the expression of genes involved in hair cells, brain, spinal cord, and fin regeneration (e.g., krt4, krt5, krt17, cyt1). Notably, we observed a correlation between the levels of rpl3 and rps7 genes, both important ribosomal proteins, and the detected alternative splicing events. Overall, this study enhances our understanding of the toxicity of beta-lactam antibiotics in zebrafish by demonstrating the developmental effects of monobactams and uncovering the underlying mechanisms at the molecular level. It also identifies potential targets for further investigation into the mechanisms of toxicity and provides valuable insights for early assessment of biological toxicity associated with antibiotic pollutants.
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Peixe-Zebra , Antibióticos beta Lactam , Animais , Peixe-Zebra/genética , Simulação de Acoplamento Molecular , Antibacterianos/química , Monobactamas , AztreonamRESUMO
BACKGROUND: Pituitary adenylate cyclase-activating polypeptide is a neuropeptide with diverse roles in biological processes. Its involvement in the blood coagulation cascade is unclear. OBJECTIVES: This study unraveled adcyap1b's role in blood coagulation using clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 in zebrafish. Effects were validated via adcyap1b knockdown. Gene expression changes in adcyap1b mutants were explored, linking them to clotting disorders. An analysis of proca gene splicing illuminated its role in adcyap1b-related anticoagulation deficiencies. METHODS: Zebrafish were genetically modified using clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 to induce adcyap1b knockout. Morpholino-mediated gene knockdown was employed for validation. Expression levels of coagulation factors, anticoagulant proteins, and fibrinolytic system genes were assessed in adcyap1b mutant zebrafish. Alternative splicing of proca gene was analyzed. RESULTS: Adcyap1b mutant zebrafish exhibited severe hemorrhage, clotting disorders, and disrupted blood coagulation. Morpholino-mediated knockdown replicated observed phenotypes. Downregulation in transcripts related to coagulation factors V and IX, anticoagulation protein C, and plasminogen was observed. Abnormal alternative splicing of the proca gene was identified, providing a mechanistic explanation for anticoagulation system deficiencies. CONCLUSION: Adcyap1b plays a crucial role in maintaining zebrafish blood coagulation and hemostasis. Its influence extends to the regulation of procoagulant and anticoagulant pathways, with abnormal alternative splicing contributing to observed deficiencies. These findings unveil a novel aspect of adcyap1b function, offering potential insights into similar processes in mammalian systems.
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Proteínas de Peixe-Zebra , Peixe-Zebra , Animais , Peixe-Zebra/genética , Peixe-Zebra/metabolismo , Proteínas de Peixe-Zebra/genética , Proteínas de Peixe-Zebra/metabolismo , Proteína 9 Associada à CRISPR/metabolismo , Morfolinos/genética , Morfolinos/metabolismo , Coagulação Sanguínea/genética , Fator V/metabolismo , Hemorragia , Anticoagulantes/metabolismo , Mamíferos/metabolismoRESUMO
BACKGROUND: More and more studies show that lncRNA is widely involved in various physiological processes of the organism. However, the functions of the vast majority of them continue to be unknown. In addition, data related to lncRNAs in biological databases are constantly increasing. Therefore, it is quite urgent to develop a computing method to make the utmost of these data. RESULTS: In this paper, we propose a new computational method based on global heterogeneous networks to predict the functions of lncRNAs, called DNGRGO. DNGRGO first calculates the similarities among proteins, miRNAs, and lncRNAs, and annotates the functions of lncRNAs according to its similar protein-coding genes, which have been labeled with gene ontology (GO). To evaluate the performance of DNGRGO, we manually annotated GO terms to lncRNAs and implemented our method on these data. Compared with the existing methods, the results of DNGRGO show superior predictive performance of maximum F-measure and coverage. CONCLUSIONS: DNGRGO is able to annotate lncRNAs through capturing the low-dimensional features of the heterogeneous network. Moreover, the experimental results show that integrating miRNA data can help to improve the predictive performance of DNGRGO.
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MicroRNAs , RNA Longo não Codificante , RNA Longo não Codificante/genética , RNA Longo não Codificante/metabolismo , Biologia Computacional/métodos , Redes Neurais de Computação , MicroRNAs/genética , MicroRNAs/metabolismo , Proteínas/metabolismo , Redes Reguladoras de GenesRESUMO
A series of new monobactam sulfonates is continuously synthesized and evaluated for their antimicrobial efficacies against Gram-negative bacteria. Compound 33a (IMBZ18G) is highly effective in vitro and in vivo against clinically intractable multi-drug-resistant (MDR) Gram-negative strains, with a highly druglike nature. The checkerboard assay reveals its significant synergistic effect with ß-lactamase inhibitor avibactam, and the MIC values against MDR enterobacteria were reduced up to 4-512 folds. X-ray co-crystal and chemoproteomic assays indicate that the anti-MDR bacteria effect of 33a results from the dual inhibition of the common PBP3 and some class A and C ß-lactamases. Accordingly, preclinical studies of 33a alone and 33aâavibactam combination as potential innovative candidates are actively going on, in the treatment of ß-lactamase-producing MDR Gram-negative bacterial infections.
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With the continuous development of ribosome profiling, sequencing technology, and proteomics, evidence is mounting that noncoding RNA (ncRNA) may be a novel source of peptides or proteins. These peptides and proteins play crucial roles in inhibiting tumor progression and interfering with cancer metabolism and other essential physiological processes. Therefore, identifying ncRNAs with coding potential is vital to ncRNA functional research. However, existing studies perform well in classifying ncRNAs and mRNAs, and no research has been explicitly raised to distinguish whether ncRNA transcripts have coding potential. For this reason, we propose an attention mechanism-based bidirectional LSTM network called ABLNCPP to assess the coding possibility of ncRNA sequences. Considering the sequential information loss in previous methods, we introduce a novel nonoverlapping trinucleotide embedding (NOLTE) method for ncRNAs to obtain embeddings containing sequential features. The extensive evaluations show that ABLNCPP outperforms other state-of-the-art models. In general, ABLNCPP overcomes the bottleneck of ncRNA coding potential prediction and is expected to provide valuable contributions to cancer discovery and treatment in the future. The source code and data sets are freely available at https://github.com/YinggggJ/ABLNCPP.
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Memória de Curto Prazo , RNA não Traduzido , RNA não Traduzido/genética , RNA não Traduzido/metabolismo , Software , PeptídeosRESUMO
Damage to vascular endothelial cells (VECs) and vascular smooth muscle cells (VSMCs) caused by oxidized low-density lipoprotein (oxLDL) contributes to cardiovascular and cerebrovascular diseases. Protection effects of Berberine (BBR) on the cardiovascular system have been reported, however, the molecular mechanism of vascular protection is still unclear. In this study, we established two hyperlipidemia models in zebrafish and VEC-VSMC co-culture using high-cholesterol food (HCF) and oxLDL, respectively. We demonstrated that HCF doubled total cholesterol and total glyceride levels, and BBR decreased these indices in a concentration-dependent manner. Lipid staining and hematoxylin-eosin staining revealed that BBR inhibited oxLDL-induced VSMC bulge-like proliferation and migration toward VECs and prevented the HCF-induced trunk vascular obstruction in zebrafish. Immunoblot analysis, cell immunofluorescence, co-immunoprecipitation assays, and transmission electron microscopy showed that oxLDL/HCF increased lectin-like oxLDL receptor-1 (LOX-1) expression at least 5-fold and significantly inhibited autophagolysosome formation in the blood vessel cells and in zebrafish. These observations were associated with endothelial-to-mesenchymal transition (EMT) in VECs and triggered VE-cadherin ectopic expression in VSMCs, and they were responsible for aberrant VSMC migration and vascular occlusion. However, BBR, by promoting autolysosome formation and degradation of LOX-1, reversed the above events and maintained intracellular homeostasis of vessel cells and vascular integrity. In conclusion, regulation of autophagy may be an effective approach to treating oxLDL-induced cardiovascular diseases by reducing LOX-1 protein level. BBR can protect blood vessels by adjusting the oxLDL-LOX-1-EMT-autophagy axis. This study is a step toward the development of new applications of BBR.
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Berberina , Animais , Berberina/farmacologia , Berberina/uso terapêutico , Peixe-Zebra/metabolismo , Células Endoteliais/metabolismo , Lipoproteínas LDL/metabolismo , Lipoproteínas LDL/farmacologia , Autofagia/genética , Receptores Depuradores Classe E/metabolismo , Colesterol/metabolismoRESUMO
The most commonly reported side effect of azithromycin is gastrointestinal (GI) disorders, and the main acid degradation product is 3'-Decladinosyl azithromycin (impurity J). We aimed to compare the GI toxicity of azithromycin and impurity J on zebrafish larvae and investigate the mechanism causing the differential GI toxicity. Results of our study showed that the GI toxicity induced by impurity J was higher than that of azithromycin in zebrafish larvae, and the effects of impurity J on transcription in the digestive system of zebrafish larvae were significantly stronger than those of azithromycin. Additionally, impurity J exerts stronger cytotoxic effects on GES-1 cells than azithromycin. Simultaneously, impurity J significantly increased ghsrb levels in the zebrafish intestinal tract and ghsr levels in human GES-1 cells compared to azithromycin, and ghsr overexpression significantly reduced cell viability, indicating that GI toxicity induced by azithromycin and impurity J may be correlated with ghsr overexpression induced by the two compounds. Meanwhile, molecular docking analysis showed that the highest -CDOCKER interaction energy scores with the zebrafish GHSRb or human GHSR protein might reflect the effect of azithromycin and impurity J on the expression of zebrafish ghsrb or human ghsr. Thus, our results suggest that impurity J has higher GI toxicity than azithromycin due to its greater ability to elevate ghsrb expression in zebrafish intestinal tract.
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Azitromicina , Peixe-Zebra , Animais , Humanos , Azitromicina/toxicidade , Larva , Simulação de Acoplamento Molecular , IntestinosRESUMO
Brucine (BRU) and brucine N-oxide (BNO) are prominent, bioactive, and toxic alkaloids in crude and processed Semen Strychni. Studies have demonstrated that BRU and BNO possess comprehensive pharmacological activities, such as anti-inflammatory and analgesic. In this context, a comparative study of BRU and BNO was performed by combination analysis of in silico ADMET prediction, in vivo toxicity evaluation, and potential action mechanism exploration. ADMET prediction showed that BRU and BNO might induce liver injury, and BRU may have a stronger hepatoxic effect. The prediction was experimentally verified using the zebrafish model. The BRU-induced hepatotoxicity of zebrafish larvae had a dose-response relationship. The mechanism of BRU-induced hepatotoxicity might relate to phosphorylation, kinase activity, and signal transduction. By comparison, signal transduction and gap junctions might involve BNO-induced hepatotoxicity. Our results provided a better understanding of BRU- and BNO-induced hepatotoxicity. We also built a foundation to elucidate the material base of the hepatotoxicity of traditional Chinese medicine Semen Strychni.
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Doença Hepática Induzida por Substâncias e Drogas , Medicamentos de Ervas Chinesas , Animais , Peixe-Zebra , Estricnina/toxicidadeRESUMO
Isatropolones/isarubrolones are Streptomyces secondary metabolites featuring a tropolone ring in the pentacyclic scaffolds of these molecules. They are able to induce complete autophagy in human HepG2 cells. Here, methyl isatropolones (1-2) and isarubrolone (3) are identified from Streptomyces CPCC 204095. They all have a methyl tropolone ring in the pentacyclic scaffold of these molecules resolved by MS and NMR spectra. Biological activity assay indicates that isatropolone Cm (1) and isarubrolone Cm (3) induce incomplete autophagy in human HepG2 cells.
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Streptomyces , Humanos , Autofagia , Espectroscopia de Ressonância Magnética , Streptomyces/metabolismo , Tropolona/farmacologia , Tropolona/metabolismoRESUMO
Statins are prescribed widely as lipid-lowering agents. However, statins are associated with an increased harmful risk on public health and the ecosystem. Little is known about statins' toxicity on biological development and the underlying molecular mechanisms. We exposed zebrafish embryos to a series of statins to evaluate their development toxicity. Statins-induced embryonic developmental defects in a concentration-dependent manner. 72 h LC50 values for lovastatin, simvastatin, fluvastatin, atorvastatin, rosuvastatin, and pravastatin were 0.01 µM, 0.04 µM, 1.93 µM, 37.28 µM, 79.29 µM, and 2170 µM, respectively. Moreover, the expression of genes involved in heart contraction, calcium ion binding, transcription factors, nucleus, and G protein-coupled receptor signaling pathway was altered by statins. The early growth response gene (egr4) and transcription factor genes (fosab and fosb) were screened as potential toxicity targets due to their significant upregulation based on protein-protein interaction (PPI) and drug-gene interaction network analysis. Finally, the ecotoxicity profile of statins was predicted by in silico method, and statins were high or moderate risk to aquatic organisms. We provide a systems toxicology strategy to explore the toxicity of statins and illustrate the potential mechanisms of action.
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Inibidores de Hidroximetilglutaril-CoA Redutases , Animais , Ecossistema , Ácidos Graxos Monoinsaturados , Inibidores de Hidroximetilglutaril-CoA Redutases/toxicidade , Indóis , Sinvastatina , Transcriptoma , Peixe-Zebra/genéticaRESUMO
Background: Chronic inflammation contributes to approximately 20% of cancers; the underlying mechanisms are still elusive. Here, using an animal model of colitis to colon-cancerous transformation, we demonstrated that endoplasmic reticulum (ER) stress couples with metabolic reprogramming to promote a malignant transformation of chronic inflammation. Methods: The animal model for chronic colitis to colon-cancerous transformation was established in C57BL/6N mice by azoxymethane (AOM) and dextran sodium sulfate (DSS) treatments. The differential proteins in control and AOM/DSS-treated colon mucosa were determined using proteomic analysis; the kinetics of metabolic modifications were monitored by mitochondrial oxygen flux, extracellular acidification, and targeted metabolomics; the molecule linker between ER stress and metabolic modifications were identified by coimmunoprecipitation, KEGG pathway analysis, and the subcutaneous tumor model using gene-specific knockdown colon cancer cells. Tissue array analysis were used to evaluate the differential protein in cancer and cancer-adjacent tissues. Results: AOM/DSS treatment induced 38 tumors in 10 mice at the 14th week with the mean tumor size 9.35 ± 3.87 mm2, which was significantly decreased to 5.85 ± 0.95 mm2 by the ER stress inhibitor 4-phenylbutyric acid (4PBA). Seven differential proteins were determined from control (1,067 ± 48) and AOM/DSS-treated mucosa (1,077 ± 59); the level of ER protein PDIA2 (protein disulfide isomerase-associated 2) was increased over 7-fold in response to AOM/DSS treatment. PDIA2 interacted with 420 proteins that were involved in 8 signaling pathways, in particular with 53 proteins in metabolic pathways. PDIA2 translocated from ER to mitochondria and interacted with the components of complexes I and II to inhibit oxophosphorylation but increase glycolysis. Knockdown PDIA2 in colon cancer cells restored the metabolic imbalance and significantly repressed tumor growth in the xenograft animal model. 4PBA therapy inhibited the AOM/DSS-mediated overexpression of PDIA2 and metabolic modifications and suppressed colon cancer growth. In clinic, PDIA2 was overexpressed in colon cancer tissues rather than cancer-adjacent tissues and was related with the late stages and lymph node metastasis of colon cancer. Conclusions: Persistent ER stress reprograms the metabolism to promote the malignant transformation of chronic colitis; PDIA2 serves as a molecule linker between ER stress and metabolic reprogramming. The inhibition of ER stress restores metabolic homeostasis and attenuates the cancerous transformation of chronic inflammation.
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BACKGROUND: Doxorubicin (DOX)-induced cardiotoxicity is related to abnormal autophagy and apoptosis in the heart. Berberine (BBR) is a well-known natural compound with potential cardioprotective and autophagic modulatory properties. HYPOTHESIS: We hypothesized that BBR ameliorates DOX-induced cardiotoxicity by balancing cardiomyocyte autophagy and apoptosis. STUDY DESIGN/METHODS: DOX was used to generate in vivo and in vitro cardiotoxic models. Larval and adult zebrafish and human AC16 cells were used to study (i) the effects of BBR on autophagy and apoptosis upon DOX challenge and (ii) the underlying mechanisms. RESULTS: BBR protected AC16 cells and zebrafish hearts from DOX-induced cytotoxicity and apoptosis. Bcl-xL knockdown in AC16 cells and zebrafish demonstrated that Bcl-xL is required for BBR's anti-apoptotic activity. DOX treatment promoted Beclin1 binding to Bcl-xL, disrupted mitophagy, and increased ROS accumulation in AC16 cells. In AC16 cells and zebrafish hearts, pretreatment with BBR enhanced mitophagy via dissociation of the Bcl-xL-Beclin1 complex and decreased ROS accumulation. Inhibition of autophagy attenuated this effect of BBR. Intriguingly, BBR increased Bcl-xL binding to Bnip3, sequestration, and mitophagy, indicating that Bcl-xL may play a beneficial role in BBR-induced mitophagy. Additionally, BBR significantly ameliorated DOX-induced cardiac dysfunction in zebrafish, whereas Bcl-xL knockdown abolished this effect. Notably, we discovered that BBR exerts biphasic dose-response effects in response to DOX; the cardioprotective properties were observed upon treatment with low-dose BBR (≤ 1 µM in cells, ≤ 10 µM in zebrafish), but not with relatively high-dose BBR. CONCLUSION: These findings indicate that the protective effects of low-dose BBR against DOX-induced cardiotoxicity are mediated by Bcl-xL.
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Berberina , Cardiotoxicidade , Animais , Apoptose , Proteína Beclina-1/metabolismo , Berberina/farmacologia , Cardiotoxicidade/tratamento farmacológico , Cardiotoxicidade/metabolismo , Doxorrubicina/farmacologia , Mitofagia , Miócitos Cardíacos , Espécies Reativas de Oxigênio/metabolismo , Peixe-Zebra/metabolismoRESUMO
BACKGROUND: Circular RNAs (circRNAs) play essential roles in cancer development and therapy resistance. Many studies have shown that circRNA is closely related to human health. The expression of circRNAs also affects the sensitivity of cells to drugs, thereby significantly affecting the efficacy of drugs. However, traditional biological experiments are time-consuming and expensive to validate drug-related circRNAs. Therefore, it is an important and urgent task to develop an effective computational method for predicting unknown circRNA-drug associations. RESULTS: In this work, we propose a computational framework (GATECDA) based on graph attention auto-encoder to predict circRNA-drug sensitivity associations. In GATECDA, we leverage multiple databases, containing the sequences of host genes of circRNAs, the structure of drugs, and circRNA-drug sensitivity associations. Based on the data, GATECDA employs Graph attention auto-encoder (GATE) to extract the low-dimensional representation of circRNA/drug, effectively retaining critical information in sparse high-dimensional features and realizing the effective fusion of nodes' neighborhood information. Experimental results indicate that GATECDA achieves an average AUC of 89.18% under 10-fold cross-validation. Case studies further show the excellent performance of GATECDA. CONCLUSIONS: Many experimental results and case studies show that our proposed GATECDA method can effectively predict the circRNA-drug sensitivity associations.
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Neoplasias , RNA Circular , Biologia Computacional/métodos , Humanos , Neoplasias/tratamento farmacológico , Neoplasias/genética , RNA Circular/genéticaRESUMO
Tryptophan (Trp) as an essential amino acid plays critical roles in regulating multiple cell activities, and the changes of its circulating level usually indicate disease status such as the severity of acute inflammation sepsis. However, the current technology for Trp detection mostly relies on chromatography that cannot meet the rapid and simple detection requirement in monitoring sepsis. Herein, a label-free fluorescent nanosensor was constructed to detect Trp and its carrier protein - human serum albumin (HSA) in plasma. The nanosensor consists of a cytosine (C) - rich signal probe of DNA-templated silver nanoclusters (AgNCs/DNA) and a Trp (Trp) aptamer - based capture probe with a guanine (G) - rich overhang. Trp was found to trigger G-rich sequence-mediated fluorescence enhancement effect for AgNCs/DNA under UV irradiation which offers energy to induce the redox process between limited Trp and silver ions bound on the DNA probes. Based on this photochemical property, the nanosensor exhibited a linear response in the range of 0.05-60 µM with the limit of detection of 0.43 µM for Trp, superior to the current fluorescence-based detection method, and it gave specific response to indole group. When applied in plasma detection, the nanosensor resisted physiological level of NaCl in plasma, but was quenched by trace volume of HSA, which facilitates the combined HSA detection using only 1 µL plasma sample. The simple procedure of "mix, exposure and detection" together with its ultralow sampling volume, time-saving, cost-effective, sensitive and selective properties endow the nanosensor great potentials for future Trp detection-based clinical use.