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1.
Phytomedicine ; 128: 155519, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38492365

RESUMO

BACKGROUND: Depression is a common mental illness characterised by abnormal and depressed emotions. Total paeony glycoside (TPG) is a naturally active saponin extracted from the traditional Chinese medicine Radix Paeoniae rubra. However, the antidepressant and neuroinflammatory effects of TPG have not been thoroughly studied. PURPOSE: To study the therapeutic potential of TGP in depression caused by neuronal injury and neuroinflammation and to explore the mechanism of TGP and the relationship between the NLRP3 inflammasome, pyroptosis, and autophagy. STUDY DESIGN: A chronic unpredictable mild stress (CUMS)-induced depression model and a cell model of corticosterone (CORT)-induced hippocampal neuron injury were established to evaluate the therapeutic effects of TPG. METHODS: The composition of TPG was analysed using high-performance liquid chromatography and mass spectrometry. The effects of TPG and fluoxetine on depression-like behaviour, neuronal injury, neuroinflammation, pyroptosis, and mitochondrial autophagy in the mice models were evaluated. RESULTS: TGP alleviated depression-like behaviours in mice and inhibited hippocampal neuronal apoptosis. The secretion of inflammatory cytokines was significantly reduced in CORT-induced hippocampal neuron cells and in the serum of a mouse model of CUMS-induced depression. In addition, TGP treatment reduced the levels of NLRP3 family pyrin structural domains, including NLRP3, pro-caspase-1, caspase-1, and IL-1ß, and the pyroptosis related proteins such as GSDMD-N. Importantly, TPG attenuated mitochondrial dysfunction, promoted the clearance of damaged mitochondria, and the activation of mitochondrial autophagy, which reduced ROS accumulation and NLRP3 inflammasome activation. An in-depth study observed that the regulatory effect of TPG on autophagy was attenuated by the autophagy inhibitor 3-methyladenine (3-MA) in vitro and in vivo. However, administration of the caspase-1 inhibitor Belnacasan (VX-765) successfully inhibited pyroptosis and showed a synergistic therapeutic effect with TPG. CONCLUSION: These results indicate that TPG can repair neuronal damage by activating autophagy, restoring mitochondrial function, and reducing inflammation-mediated pyroptosis, thereby playing an important role in the alleviation of neuroinflammation and depression. This study suggests new potential drugs and treatment strategies for neuroinflammation-related diseases and depression.


Assuntos
Antidepressivos , Autofagia , Depressão , Modelos Animais de Doenças , Glicosídeos , Hipocampo , Inflamassomos , Proteína 3 que Contém Domínio de Pirina da Família NLR , Paeonia , Piroptose , Animais , Proteína 3 que Contém Domínio de Pirina da Família NLR/metabolismo , Autofagia/efeitos dos fármacos , Antidepressivos/farmacologia , Inflamassomos/metabolismo , Inflamassomos/efeitos dos fármacos , Camundongos , Masculino , Glicosídeos/farmacologia , Piroptose/efeitos dos fármacos , Hipocampo/efeitos dos fármacos , Hipocampo/metabolismo , Depressão/tratamento farmacológico , Paeonia/química , Camundongos Endogâmicos C57BL , Neurônios/efeitos dos fármacos , Doenças Neuroinflamatórias/tratamento farmacológico , Medicamentos de Ervas Chinesas/farmacologia
2.
Sci Rep ; 14(1): 4122, 2024 Feb 19.
Artigo em Inglês | MEDLINE | ID: mdl-38374398

RESUMO

Message passing neural networks such as graph convolutional networks (GCN) can jointly consider various types of features for social bot detection. However, the expressive power of GCN is upper-bounded by the 1st-order Weisfeiler-Leman isomorphism test, which limits the detection performance for the social bots. In this paper, we propose a subgraph encoding based GCN model, SEGCN, with stronger expressive power for social bot detection. Each node representation of this model is computed as the encoding of a surrounding induced subgraph rather than encoding of immediate neighbors only. Extensive experimental results on two publicly available datasets, Twibot-20 and Twibot-22, showed that the proposed model improves the accuracy of the state-of-the-art social bot detection models by around 2.4%, 3.1%, respectively.

3.
Cell Mol Biol (Noisy-le-grand) ; 70(1): 110-118, 2024 Jan 31.
Artigo em Inglês | MEDLINE | ID: mdl-38372104

RESUMO

The salivary gland (SGS) is a kind of organ vulnerable to ionizing radiation. Radiotherapy is an important treatment for head and neck tumors, but in the process of radiotherapy, tumor cells will be injured by radiation to a certain extent. Infrared-induced DNA double-strand break (IR-DSBs) is one of the most serious DNA damage. DNA repair proteins such as Nymegan rupture syndrome protein 1 (NBS1) play a key role in the identification and repair of DNA damage. but the interaction between SSB1 and NBS1 has not been elucidated. In this study, we irradiated rat submandibular gland (SMG) cells, which were either infected with a rAdE5-SSB1-1p2-shRNA recombinant adenovirus to silence SSB or a control virus, to explore the effect of IR on the expression NBS1 in the absence of SSB. Our results showed that the SSB1 mRNA transcripts and protein expression of SSB1 and NBS1 initially increased and decreased later with increased doses. The relative expression reached the highest levels when the SMG cells were irradiated with 2Gy of IR. Silencing the SSB1 gene suppressed the expression of both SSB1 and NBS1 regardless of irradiation. The expression of NBS1 decreased when the SSB1 gene was silenced. We concluded that IR affected the expression of both SSB1 and NBS1 and there is a synergistic effect on IR-induced NBS1 suppression and DSBs repair in SMG cells. These observations shed light on further investigation and elucidation of IR-caused DNA repair mechanisms.


Assuntos
Proteínas de Ciclo Celular , Proteínas Nucleares , Glândula Submandibular , Animais , Ratos , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Dano ao DNA , Reparo do DNA/genética , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Glândula Submandibular/metabolismo
4.
Adv Drug Deliv Rev ; 203: 115144, 2023 12.
Artigo em Inglês | MEDLINE | ID: mdl-37995899

RESUMO

In recent years, RNA-based therapies have gained much attention as biomedicines due to their remarkable therapeutic effects with high specificity and potency. Lung diseases offer a variety of currently undruggable but attractive targets that could potentially be treated with RNA drugs. Inhaled RNA drugs for the treatment of lung diseases, including asthma, chronic obstructive pulmonary disease, cystic fibrosis, and acute respiratory distress syndrome, have attracted more and more attention. A variety of novel nanoformulations have been designed and attempted for the delivery of RNA drugs to the lung via inhalation. However, the delivery of RNA drugs via inhalation poses several challenges. It includes protection of the stability of RNA molecules, overcoming biological barriers such as mucus and cell membrane to the delivery of RNA molecules to the targeted cytoplasm, escaping endosomal entrapment, and circumventing unwanted immune response etc. To address these challenges, ongoing researches focus on developing innovative nanoparticles to enhance the stability of RNA molecules, improve cellular targeting, enhance cellular uptake and endosomal escape to achieve precise delivery of RNA drugs to the intended lung cells while avoiding unwanted nano-bio interactions and off-target effects. The present review first addresses the pathologic hallmarks of different lung diseases, disease-related cell types in the lung, and promising therapeutic targets in these lung cells. Subsequently we highlight the importance of the nano-bio interactions in the lung that need to be addressed to realize disease-related cell-specific delivery of inhaled RNA drugs. This is followed by a review on the physical and chemical characteristics of inhaled nanoformulations that influence the nano-bio interactions with a focus on surface functionalization. Finally, the challenges in the development of inhaled nanomedicines and some key aspects that need to be considered in the development of future inhaled RNA drugs are discussed.


Assuntos
Asma , Fibrose Cística , Pneumopatias , Doença Pulmonar Obstrutiva Crônica , Humanos , RNA/metabolismo , Pneumopatias/tratamento farmacológico , Pneumopatias/metabolismo , Doença Pulmonar Obstrutiva Crônica/tratamento farmacológico , Pulmão/metabolismo , Fibrose Cística/tratamento farmacológico , Asma/tratamento farmacológico , Preparações Farmacêuticas/metabolismo , Administração por Inalação , Sistemas de Liberação de Medicamentos
5.
Phys Med Biol ; 68(14)2023 07 10.
Artigo em Inglês | MEDLINE | ID: mdl-37336207

RESUMO

This paper presents a simulation study to demonstrate that the contrast recovery coefficients (CRC) and detectability of small lesions of a one-meter-long positron emission tomography (PET) scanner can be further enhanced by the integration of high resolution virtual-pinhole (VP) PET devices. The scanner under investigation is a Siemens Biograph Vision Quadra which has an axial field-of-view (FOV) of 106 cm. The VP-PET devices contain two high-resolution flat panel detectors, each composed of 2 × 8 detector modules each of which consists of 32 × 64 lutetium-oxyorthosilicate crystals (1.0 × 1.0 × 10.0 mm3each). Two configurations for the VP-PET device placement were evaluated: (1) place the two flat-panel detectors at the center of the scanner's axial FOV below the patient bed; (2) place one flat-panel detector at the center of the first and the last quarter of the scanner's axial FOV below the patient bed. Sensitivity profiles were measured by moving a point22Na source stepwise across the scanner's FOV axially at different locations. To assess the improvement in CRC and lesion detectability by the VP-PET devices, an elliptical torso phantom (31.6 × 22.8 × 106 cm3) was first imaged by the native scanner then subsequently by the two VP-PET geometry configurations. Spherical lesions (4 mm in diameter) having 5:1 lesion-to-background radioactivity concentration ratio were grouped and placed at nine regions in the phantom to analyze the dependence of the improvement in plane. Average CRCs and their standard deviations of the 7 tumors in each group were computed and the receiver operating characteristic (ROC) curves were drawn to evaluate the improvement in lesion detectability by the VP-PET device over the native long axial PET scanner. The fraction of coincidence events between the inserts and the scanner detectors was 13%-16% (out of the total number of coincidences) for VP-PET configuration 1 and 2, respectively. The VP-PET systems provide higher CRCs for lesions in all regions in the torso, with more significant enhancement at regions closer to the inserts, than the native scanner does. For any given false positive fraction, the VP-PET systems offer higher true positive fraction compared to the native scanner. This work provides a potential solution to further enhance the image resolution of a long axial FOV PET scanner to maximize its lesion detectability afforded by its super high effective sensitivity.


Assuntos
Processamento de Imagem Assistida por Computador , Tomografia Computadorizada por Raios X , Humanos , Tomografia por Emissão de Pósitrons/métodos , Imagens de Fantasmas , Simulação por Computador
6.
J Int Med Res ; 51(6): 3000605231182547, 2023 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-37377087

RESUMO

OBJECTIVE: Evidence of therapy for dysfunctional coronary circulation in patients with ST-segment elevation myocardial infarction (STEMI) undergoing primary percutaneous coronary intervention (pPCI) is limited. This study was performed to compare the effects of atorvastatin and rosuvastatin on dysfunctional coronary circulation. METHODS: This retrospective study enrolled 597 consecutive patients with STEMI who underwent pPCI in 3 centers from June 2016 to December 2019. Dysfunctional coronary circulation was defined by the thrombolysis in myocardial infarction (TIMI) grade and the TIMI myocardial perfusion grade (TMPG). Logistic regression analysis was used to evaluate the impact of different statin types on dysfunctional coronary circulation. RESULTS: The incidence of TIMI no/slow reflow did not differ between the two groups, but the incidence of TMPG no/slow reflow was significantly lower in the atorvastatin than rosuvastatin group (44.58% vs. 57.69%, respectively). After multivariate adjustment, the odds ratio with 95% confidence interval of rosuvastatin was 1.72 (1.17-2.52) for after pretreatment TMPG no/slow reflow and 1.73 (1.16-2.58) for after stenting TMPG no/slow reflow. Atorvastatin and rosuvastatin showed no significant differences in clinical outcomes during hospitalization. CONCLUSIONS: Compared with rosuvastatin, atorvastatin was associated with better coronary microcirculatory perfusion in patients with STEMI who underwent pPCI.


Assuntos
Infarto do Miocárdio , Fenômeno de não Refluxo , Intervenção Coronária Percutânea , Infarto do Miocárdio com Supradesnível do Segmento ST , Humanos , Infarto do Miocárdio com Supradesnível do Segmento ST/tratamento farmacológico , Infarto do Miocárdio com Supradesnível do Segmento ST/cirurgia , Atorvastatina/uso terapêutico , Rosuvastatina Cálcica/uso terapêutico , Resultado do Tratamento , Estudos Retrospectivos , Microcirculação , Intervenção Coronária Percutânea/efeitos adversos , Circulação Coronária , Angiografia Coronária , Fenômeno de não Refluxo/tratamento farmacológico , Fenômeno de não Refluxo/etiologia
7.
J Control Release ; 352: 422-437, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-36265740

RESUMO

With specific and inherent mRNA cleaving activity, small interfering RNA (siRNA) has been deemed promising therapeutics to reduce the exacerbation rate of asthma by inhibiting the expression and release of proinflammatory cytokines from airway epithelial cells (AECs). To exert the therapeutic effects of siRNA drugs, nano-formulations with high efficiency and safety are required to deliver these nucleic acids to the target cells. Herein, we exploited novel inhaled lipid nanoparticles (LNPs) targeting intercellular adhesion molecule-1 (ICAM-1) receptors on the apical side of AECs. This delivery system is meant to enhance the specific delivery efficiency of siRNA in AECs to prevent the expression of proinflammatory cytokines in AECs and the concomitant symptoms in parallel. A cyclic peptide that resembles part of the capsid protein of rhinovirus and binds to ICAM-1 receptors was initially conjugated with cholesterol and subsequently assembled with ionizable cationic lipids to form the LNPs (Pep-LNPs) loaded with siRNA against thymic stromal lymphopoietin (TSLP siRNA). The obtained Pep-LNPs were subjected to thorough characterization and evaluations in vitro and in vivo. Pep-LNPs significantly enhanced cellular uptake and gene silencing efficiency in human epithelial cells expressing ICAM-1 in vitro, exhibited AEC-specific delivery and improved the gene silencing effect in ovalbumin-challenged asthmatic mice after pulmonary administration. More importantly, Pep-LNPs remarkably downregulated the expression of TSLP in AECs, effectively alleviated inflammatory cell infiltration, and reduced the secretion of other proinflammatory cytokines, including IL-4 and IL-13, as well as mucus production in asthmatic mice. This study demonstrates that Pep-LNPs are safe and efficient to deliver siRNA drugs to asthmatic AECs and could potentially alleviate allergic asthma by inhibiting the overexpression of proinflammatory cytokines in the airway.


Assuntos
Asma , Nanopartículas , Camundongos , Humanos , Animais , RNA Interferente Pequeno , Molécula 1 de Adesão Intercelular/genética , Lipídeos/química , Nanopartículas/química , RNA de Cadeia Dupla , Citocinas/genética , Asma/genética , Asma/terapia , Células Epiteliais
8.
Nat Commun ; 13(1): 3094, 2022 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-35655064

RESUMO

The fundamental goal of artificial intelligence (AI) is to mimic the core cognitive activities of human. Despite tremendous success in the AI research, most of existing methods have only single-cognitive ability. To overcome this limitation and take a solid step towards artificial general intelligence (AGI), we develop a foundation model pre-trained with huge multimodal data, which can be quickly adapted for various downstream cognitive tasks. To achieve this goal, we propose to pre-train our foundation model by self-supervised learning with weak semantic correlation data crawled from the Internet and show that promising results can be obtained on a wide range of downstream tasks. Particularly, with the developed model-interpretability tools, we demonstrate that strong imagination ability is now possessed by our foundation model. We believe that our work makes a transformative stride towards AGI, from our common practice of "weak or narrow AI" to that of "strong or generalized AI".


Assuntos
Inteligência Artificial , Inteligência , Coleta de Dados , Humanos
9.
Brief Bioinform ; 23(3)2022 05 13.
Artigo em Inglês | MEDLINE | ID: mdl-35443027

RESUMO

Predicting the binding of peptide and major histocompatibility complex (MHC) plays a vital role in immunotherapy for cancer. The success of Alphafold of applying natural language processing (NLP) algorithms in protein secondary struction prediction has inspired us to explore the possibility of NLP methods in predicting peptide-MHC class I binding. Based on the above motivations, we propose the MHCRoBERTa method, RoBERTa pre-training approach, for predicting the binding affinity between type I MHC and peptides. Analysis of the results on benchmark dataset demonstrates that MHCRoBERTa can outperform other state-of-art prediction methods with an increase of the Spearman rank correlation coefficient (SRCC) value. Notably, our model gave a significant improvement on IC50 value. Our method has achieved SRCC value and AUC value as 0.785 and 0.817, respectively. Our SRCC value is 14.3% higher than NetMHCpan3.0 (the second highest SRCC value on pan-specific) and is 3% higher than MHCflurry (the second highest SRCC value on all methods). The AUC value is also better than any other pan-specific methods. Moreover, we visualize the multi-head self-attention for the token representation across the layers and heads by this method. Through the analysis of the representation of each layer and head, we can show whether the model has learned the syntax and semantics necessary to perform the prediction task well. All these results demonstrate that our model can accurately predict the peptide-MHC class I binding affinity and that MHCRoBERTa is a powerful tool for screening potential neoantigens for cancer immunotherapy. MHCRoBERTa is available as an open source software at github (https://github.com/FuxuWang/MHCRoBERTa).


Assuntos
Antígenos de Histocompatibilidade Classe I , Peptídeos , Algoritmos , Sequência de Aminoácidos , Antígenos de Histocompatibilidade Classe I/metabolismo , Aprendizado de Máquina , Peptídeos/metabolismo , Ligação Proteica
10.
Stem Cell Res Ther ; 13(1): 160, 2022 04 11.
Artigo em Inglês | MEDLINE | ID: mdl-35410459

RESUMO

BACKGROUND: Breast carcinoma-amplified sequence 2 (BCAS2) regulates ß-catenin gene splicing. The conditional knockout of BCAS2 expression in the forebrain (BCAS2 cKO) of mice confers impaired learning and memory along with decreased ß-catenin expression. Because ß-catenin reportedly regulates adult neurogenesis, we wondered whether BCAS2 could regulate adult neurogenesis via ß-catenin. METHODS: BCAS2-regulating neurogenesis was investigated by characterizing BCAS2 cKO mice. Also, lentivirus-shBCAS2 was intracranially injected into the hippocampus of wild-type mice to knock down BCAS2 expression. We evaluated the rescue effects of BCAS2 cKO by intracranial injection of adeno-associated virus encoding BCAS2 (AAV-DJ8-BCAS2) and AAV-ß-catenin gene therapy. RESULTS: To show that BCAS2-regulating adult neurogenesis via ß-catenin, first, BCAS2 cKO mice showed low SRY-box 2-positive (Sox2+) neural stem cell proliferation and doublecortin-positive (DCX+) immature neurons. Second, stereotaxic intracranial injection of lentivirus-shBCAS2 knocked down BCAS2 in the hippocampus of wild-type mice, and we confirmed the BCAS2 regulation of adult neurogenesis via ß-catenin. Third, AAV-DJ8-BCAS2 gene therapy in BCAS2 cKO mice reversed the low proliferation of Sox2+ neural stem cells and the decreased number of DCX+ immature neurons with increased ß-catenin expression. Moreover, AAV-ß-catenin gene therapy restored neuron stem cell proliferation and immature neuron differentiation, which further supports BCAS2-regulating adult neurogenesis via ß-catenin. In addition, cells targeted by AAV-DJ8 injection into the hippocampus included Sox2 and DCX immature neurons, interneurons, and astrocytes. BCAS2 may regulate adult neurogenesis by targeting Sox2+ and DCX+ immature neurons for autocrine effects and interneurons or astrocytes for paracrine effects. CONCLUSIONS: BCAS2 can regulate adult neurogenesis in mice via ß-catenin.


Assuntos
Células-Tronco Neurais , beta Catenina , Animais , Hipocampo , Camundongos , Proteínas de Neoplasias/metabolismo , Células-Tronco Neurais/metabolismo , Neurogênese/fisiologia , Neurônios/metabolismo , beta Catenina/genética , beta Catenina/metabolismo
11.
J Diabetes Res ; 2021: 9238566, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34805413

RESUMO

BACKGROUND: Diabetes mellitus (DM) and dyslipidemia are the main risk factors for atherosclerosis. Elevated glycosylated hemoglobin A1c (HbA1c) and reduced high-density lipoprotein cholesterol (HDL-C) are associated with the progression of atherosclerosis. The aim of this study is at exploring the relationship between the HbA1c/HDL-C ratio and atherosclerosis evaluated using carotid artery intima-media thickness (cIMT) and carotid artery plaque. METHODS: In this retrospective study, we enrolled 1304 patients who had multiple cardiovascular risk factors or symptoms of suspected coronary artery disease. cIMT and carotid artery plaque were measured using ultrasonography. Logistic regression was used to explore the correlation between the HbA1c/HDL-C ratio and cIMT or carotid artery plaque. We used restricted cubic spline curves to assess nonlinear relationships between the HbA1c/HDL-C ratio and cIMT or carotid artery plaque. RESULTS: With increased quartiles of HbA1c/HDL-C, patients had higher cIMT and a greater carotid plaque burden. After adjusting for other relevant clinical covariates, patients with the highest HbA1c/HDL-C ratio (quartile 4 (Q4)) had a 2.88 times (95% confidence interval (CI): 2.02-4.10, P < 0.001) more abnormal mean cIMT, 3.72 times (95% CI: 2.55-5.44, P < 0.001) more abnormal maximum cIMT, and 2.58 times (95% CI: 1.70-3.91, P < 0.001) greater carotid artery plaque burden compared with patients who had the lowest HbA1c/HDL-C ratio (Q1). Moreover, the association of HbA1c/HDL-C with atherosclerosis remained significant in a subsample of patients with and without DM. CONCLUSION: As a novel compound indicator for evaluating blood glucose homeostasis and dyslipidemia, the HbA1c/HDL-C ratio was positively correlated with carotid atherosclerosis evaluated using the mean and maximum cIMT as well as the carotid artery plaque burden.


Assuntos
Glicemia/análise , Doenças das Artérias Carótidas/sangue , HDL-Colesterol/sangue , Diabetes Mellitus/sangue , Dislipidemias/sangue , Hemoglobinas Glicadas/análise , Idoso , Biomarcadores/sangue , Doenças das Artérias Carótidas/diagnóstico por imagem , Espessura Intima-Media Carotídea , Diabetes Mellitus/diagnóstico , Dislipidemias/diagnóstico , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Placa Aterosclerótica , Valor Preditivo dos Testes , Estudos Retrospectivos , Medição de Risco , Fatores de Risco
12.
Front Genet ; 12: 745224, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34745219

RESUMO

Significant genetic association exists between rheumatoid arthritis (RA) and cardiovascular disease. The associated mechanisms include common inflammatory mediators, changes in lipoprotein composition and function, immune responses, etc. However, the causality of RA and vascular/heart problems remains unknown. Herein, we performed Mendelian randomization (MR) analysis using a large-scale RA genome-wide association study (GWAS) dataset (462,933 cases and 457,732 controls) and six cardio-cerebrovascular disease GWAS datasets, including age angina (461,880 cases and 447,052 controls), hypertension (461,880 cases and 337,653 controls), age heart attack (10,693 cases and 451,187 controls), abnormalities of heartbeat (461,880 cases and 361,194 controls), stroke (7,055 cases and 454,825 controls), and coronary heart disease (361,194 cases and 351,037 controls) from United Kingdom biobank. We further carried out heterogeneity and sensitivity analyses. We confirmed the causality of RA with age angina (OR = 1.17, 95% CI: 1.04-1.33, p = 1.07E-02), hypertension (OR = 1.45, 95% CI: 1.20-1.75, p = 9.64E-05), age heart attack (OR = 1.15, 95% CI: 1.05-1.26, p = 3.56E-03), abnormalities of heartbeat (OR = 1.07, 95% CI: 1.01-1.12, p = 1.49E-02), stroke (OR = 1.06, 95% CI: 1.01-1.12, p = 2.79E-02), and coronary heart disease (OR = 1.19, 95% CI: 1.01-1.39, p = 3.33E-02), contributing to the understanding of the overlapping genetic mechanisms and therapeutic approaches between RA and cardiovascular disease.

13.
Front Cell Dev Biol ; 9: 710566, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34211980

RESUMO

[This corrects the article DOI: 10.3389/fcell.2021.643582.].

14.
Front Cell Dev Biol ; 9: 643582, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33791302

RESUMO

The etiology of non-alcoholic fatty liver disease (NAFLD) involves complex interaction of genetic and environmental factors. A large number of observational studies have shown that hypothyroidism contributes to a high risk of NAFLD. However, the exact causality is still unknown. Due to the progress of genome-wide association study (GWAS) and the discovery of Mendelian randomization (MR), it is possible to explore the causality between the two diseases. In this study, in order to research into the influence of intermediate phenotypes on outcome, nine independent genetic variants of hypothyroidism obtained from the GWAS were used as instrumental variables (IVs) to perform MR analysis on NAFLD. Since there was no heterogeneity between IVs (P = 0.70), a fixed-effects model was used. The correlation between hypothyroidism and NAFLD was evaluated by using inverse-variance weighted (IVW) method and weighted median method. Then the sensitivity test was analyzed. The results showed that there was a high OR (1.7578; 95%CI 1.1897-2.5970; P = 0.0046) and a low intercept (-0.095; P = 0.431). None of the genetic variants drove the overall result (P < 0.01). Simply, we proved for the first time that the risk of NAFLD increases significantly on patients with hypothyroidism. Furthermore, we explained possible causes of NAFLD caused by hypothyroidism.

15.
PLoS Comput Biol ; 16(12): e1008543, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-33378330

RESUMO

Computational methods that predict protein stability changes induced by missense mutations have made a lot of progress over the past decades. Most of the available methods however have very limited accuracy in predicting stabilizing mutations because existing experimental sets are dominated by mutations reducing protein stability. Moreover, few approaches could consistently perform well across different test cases. To address these issues, we developed a new computational method PremPS to more accurately evaluate the effects of missense mutations on protein stability. The PremPS method is composed of only ten evolutionary- and structure-based features and parameterized on a balanced dataset with an equal number of stabilizing and destabilizing mutations. A comprehensive comparison of the predictive performance of PremPS with other available methods on nine benchmark datasets confirms that our approach consistently outperforms other methods and shows considerable improvement in estimating the impacts of stabilizing mutations. A protein could have multiple structures available, and if another structure of the same protein is used, the predicted change in stability for structure-based methods might be different. Thus, we further estimated the impact of using different structures on prediction accuracy, and demonstrate that our method performs well across different types of structures except for low-resolution structures and models built based on templates with low sequence identity. PremPS can be used for finding functionally important variants, revealing the molecular mechanisms of functional influences and protein design. PremPS is freely available at https://lilab.jysw.suda.edu.cn/research/PremPS/, which allows to do large-scale mutational scanning and takes about four minutes to perform calculations for a single mutation per protein with ~ 300 residues and requires ~ 0.4 seconds for each additional mutation.


Assuntos
Biologia Computacional/métodos , Mutação de Sentido Incorreto , Estabilidade Proteica , Substituição de Aminoácidos , Bases de Dados de Proteínas , Conjuntos de Dados como Assunto , Conformação Proteica , Proteínas/química
16.
Int J Mol Sci ; 21(15)2020 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-32756481

RESUMO

Protein-RNA interactions are crucial for many cellular processes, such as protein synthesis and regulation of gene expression. Missense mutations that alter protein-RNA interaction may contribute to the pathogenesis of many diseases. Here, we introduce a new computational method PremPRI, which predicts the effects of single mutations occurring in RNA binding proteins on the protein-RNA interactions by calculating the binding affinity changes quantitatively. The multiple linear regression scoring function of PremPRI is composed of three sequence- and eight structure-based features, and is parameterized on 248 mutations from 50 protein-RNA complexes. Our model shows a good agreement between calculated and experimental values of binding affinity changes with a Pearson correlation coefficient of 0.72 and the corresponding root-mean-square error of 0.76 kcal·mol-1, outperforming three other available methods. PremPRI can be used for finding functionally important variants, understanding the molecular mechanisms, and designing new protein-RNA interaction inhibitors.


Assuntos
Biologia Computacional , Proteínas de Ligação a RNA/genética , RNA/genética , Software , Fenômenos Biofísicos , Humanos , Modelos Moleculares , Mutação de Sentido Incorreto/genética , Ligação Proteica/genética
17.
iScience ; 23(3): 100939, 2020 Mar 27.
Artigo em Inglês | MEDLINE | ID: mdl-32169820

RESUMO

Missense mutations may affect proteostasis by destabilizing or over-stabilizing protein complexes and changing the pathway flux. Predicting the effects of stabilizing mutations on protein-protein interactions is notoriously difficult because existing experimental sets are skewed toward mutations reducing protein-protein binding affinity and many computational methods fail to correctly evaluate their effects. To address this issue, we developed a method MutaBind2, which estimates the impacts of single as well as multiple mutations on protein-protein interactions. MutaBind2 employs only seven features, and the most important of them describe interactions of proteins with the solvent, evolutionary conservation of the site, and thermodynamic stability of the complex and each monomer. This approach shows a distinct improvement especially in evaluating the effects of mutations increasing binding affinity. MutaBind2 can be used for finding disease driver mutations, designing stable protein complexes, and discovering new protein-protein interaction inhibitors.

18.
Environ Geochem Health ; 41(1): 43-52, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-29948534

RESUMO

Cadmium (Cd)-contaminated rice (Oryza sativa) in Southern China is a great threat to food security, and the paddy soil remediation is urgently needed to reduce Cd accumulation in rice. Application of biochar could effectively immobilize soil Cd and reduce Cd uptake by rice. Fields that were applied with soil treatments including control and 15 and 30 t ha-1 each hickory nut shell-derived biochar (KC) or maize straw-derived biochar (MC), and grown with two rice varieties (hybrid rice and late japonica rice) were selected for this study. The long-term effect of biochars on decreasing Cd bioavailability in paddy soils was evaluated. The results showed when MC was applied at 15 t ha-1, DTPA-Cd (soil cadmium extracted by diethylenetriamine pentaacetic acid) was reduced by 20.0 and 34.5% in Field A (slightly Cd pollution) and B (moderately Cd pollution), respectively. In Field B, soil DTPA-Cd concentrations with application of 30 t ha-1 biochars were all lower than that of 15 t ha-1 biochar, but there were no significant differences between the two types of biochars. Cd concentration in rice grains and straws of hybrid rice are two times more than those of late japonica rice. Cd bio-concentration factor both of grains and straw was significantly increased by biochar application, which in Field A was higher than that in Field B. Our results suggest that biochars reduce Cd accumulation in rice grains by immobilizing soil Cd. KC has a higher potential in lowering Cd bioavailability than MC. Hybrid rice should be prohibited to cultivate in these areas.


Assuntos
Cádmio/análise , Carvão Vegetal/química , Poluição Ambiental/análise , Oryza/química , Disponibilidade Biológica , China , Mineração , Estruturas Vegetais/química , Solo/química , Poluentes do Solo/análise , Tungstênio/química , Zea mays
19.
Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi ; 33(10): 1385-1391, 2017 Oct.
Artigo em Chinês | MEDLINE | ID: mdl-29169424

RESUMO

Objective To investigate the effect of exogenous hydrogen sulfide from sodium hydrosulfide (NaHS) on cardiac thioredoxin (Trx) system in diabetic rats. Methods Male Sprague-Dawley rats were randomly divided into a normal group, a diabetic group, and three NaHS (14, 28 and 56 µmol/kg) treatment groups, with 6 rats in each group. Type 1 diabetes was induced in the groups by a single intraperitoneal (i.p.) injection of streptozotocin. At the fifth week after modeling, the NaHS treatment groups were injected (i.p.) with NaHS at the doses of 14, 28 and 56 µmol/kg once a day, respectively. After the treatment for 4 weeks, the fasting blood glucose (FBG) level and ventricular hemodynamic parameters were measured. The changes of myocardial pathomorphology were observed by HE staining. The ultrastructural changes of cardiomyocytes were observed by transmission electron microscopy. The levels of serum lactate dehydrogenase (LDH), creatine kinase (CK), and creatine kinase MB isozyme (CK-MB) were examined using the kits. Serum interleukin (IL)-1ß, IL-6, and tumor necrosis factor α (TNF-α) were assayed by ELISA. The levels of total antioxidant capacity (T-AOC), lipid peroxide (LPO), and malondialdehyde (MDA) in myocardium were analyzed using the kits. The mRNA expression of heme oxygenase 1 (HO-1) was detected using reverse transcription PCR (RT-PCR). The expression levels of Trx, Trx-interacting protein (TXNIP), and nicotinamide adenine dinucleotide phosphate oxidase 2 (NOX2) in myocardium were measured using Western blotting. Results Compared with the normal group, the left ventricular systolic and diastolic functions were weakened in the diabetic group, and the myocardial morphological structure and ultrastructure were damaged obviously. The FBG, LDH, CK, CK-MB, IL-1ß, IL-6, TNF-α, LPO and MDA levels increased, while the T-AOC level decreased. The myocardial Trx protein expression was reduced, while the expressions of HO-1 mRNA, TXNIP and NOX2 proteins were elevated in the diabetic group. Compared with the diabetic group, the left ventricular systolic and diastolic functions, myocardial morphological structure and ultrastructure were improved in the three NaHS treatment groups. The LDH, CK, CK-MB, IL-1ß, IL-6, TNF-α, LPO and MDA levels decreased, while T-AOC increased. The myocardial HO-1 mRNA and Trx protein expressions were enhanced, while TXNIP and NOX2 protein expressions were suppressed. Conclusion NaHS treatment attenuates diabetic myocardial injury, and the mechanisms may be associated with the activation of the Trx system, the enhancement of antioxidant capability and the inhibition of inflammatory factor release.


Assuntos
Diabetes Mellitus Experimental/complicações , Diabetes Mellitus Tipo 1/complicações , Cardiomiopatias Diabéticas/prevenção & controle , Sulfetos/farmacologia , Tiorredoxinas/metabolismo , Animais , Glicemia/metabolismo , Proteínas de Transporte/metabolismo , Proteínas de Ciclo Celular , Citocinas/sangue , Diabetes Mellitus Experimental/sangue , Diabetes Mellitus Tipo 1/sangue , Cardiomiopatias Diabéticas/etiologia , Cardiomiopatias Diabéticas/metabolismo , Peróxidos Lipídicos/metabolismo , Masculino , Malondialdeído/metabolismo , Microscopia Eletrônica de Transmissão , Miocárdio/metabolismo , Miocárdio/patologia , Miócitos Cardíacos/efeitos dos fármacos , Miócitos Cardíacos/metabolismo , Miócitos Cardíacos/ultraestrutura , Ratos Sprague-Dawley
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