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1.
Cell Commun Signal ; 22(1): 213, 2024 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-38566235

RESUMO

BACKGROUND: Desensitization of G protein-coupled receptors (GPCRs) refers to the attenuation of receptor responsiveness by prolonged or intermittent exposure to agonists. The binding of ß-arrestin to the cytoplasmic cavity of the phosphorylated receptor, which competes with the G protein, has been widely accepted as an extensive model for explaining GPCRs desensitization. However, studies on various GPCRs, including dopamine D2-like receptors (D2R, D3R, D4R), have suggested the existence of other desensitization mechanisms. The present study employed D2R/D3R variants with different desensitization properties and utilized loss-of-function approaches to uncover the mechanisms underlying GPCRs homologous desensitization, focusing on the signaling cascade that regulates the ubiquitination of AKT. RESULTS: AKT undergoes K8/14 ubiquitination by TRAF6, which occurs in the nucleus and promotes its membrane recruitment, phosphorylation and activation under receptor desensitization conditions. The nuclear entry of TRAF6 relies on the presence of the importin complex. Src regulates the nuclear entry of TRAF6 by mediating the interaction between TRAF6 and importin ß1. Ubiquitinated AKT translocates to the plasma membrane where it associates with Mdm2 to phosphorylate it at the S166 and S186 residues. Thereafter, phosphorylated Mdm2 is recruited to the nucleus, resulting in the deubiquitination of ß-Arr2. The deubiquitinated ß-Arr2 then forms a complex with Gßγ, which serves as a biomarker for GPCRs desensitization. Like in D3R, ubiquitination of AKT is also involved in the desensitization of ß2 adrenoceptors. CONCLUSION: Our study proposed that the property of a receptor that causes a change in the subcellular localization of TRAF6 from the cytoplasm to the nucleus to mediate AKT ubiquitination could initiate the desensitization of GPCRs.


Assuntos
Proteínas Proto-Oncogênicas c-akt , Fator 6 Associado a Receptor de TNF , Fator 6 Associado a Receptor de TNF/metabolismo , Proteínas Proto-Oncogênicas c-akt/metabolismo , Receptores Acoplados a Proteínas G/metabolismo , Ubiquitinação , Fosforilação , Carioferinas
2.
Methods ; 212: 21-30, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-36813016

RESUMO

Long non-coding RNAs are a class of essential non-coding RNAs with a length of more than 200 nts. Recent studies have indicated that lncRNAs have various complex regulatory functions, which play great impacts on many fundamental biological processes. However, measuring the functional similarity between lncRNAs by traditional wet-experiments is time-consuming and labor intensive, computational-based approaches have been an effective choice to tackle this problem. Meanwhile, most sequences-based computation methods measure the functional similarity of lncRNAs with their fixed length vector representations, which could not capture the features on larger k-mers. Therefore, it is urgent to improve the predict performance of the potential regulatory functions of lncRNAs. In this study, we propose a novel approach called MFSLNC to comprehensively measure functional similarity of lncRNAs based on variable k-mer profiles of nucleotide sequences. MFSLNC employs the dictionary tree storage, which could comprehensively represent lncRNAs with long k-mers. The functional similarity between lncRNAs is evaluated by the Jaccard similarity. MFSLNC verified the similarity between two lncRNAs with the same mechanism, detecting homologous sequence pairs between human and mouse. Besides, MFSLNC is also applied to lncRNA-disease associations, combined with the association prediction model WKNKN. Moreover, we also proved that our method can more effectively calculate the similarity of lncRNAs by comparing with the classical methods based on the lncRNA-mRNA association data. The detected AUC value of prediction is 0.867, which achieves good performance in the comparison of similar models.


Assuntos
RNA Longo não Codificante , Humanos , Animais , Camundongos , RNA Longo não Codificante/genética , Sequência de Bases , Biologia Computacional/métodos , Algoritmos
3.
Int J Mol Sci ; 24(12)2023 Jun 12.
Artigo em Inglês | MEDLINE | ID: mdl-37373182

RESUMO

A class-A GPCR dopamine D2 receptor (D2R) plays a critical role in the proper functioning of neuronal circuits through the downstream activation of both G-protein- and ß-arrestin-dependent signaling pathways. Understanding the signaling pathways downstream of D2R is critical for developing effective therapies with which to treat dopamine (DA)-related disorders such as Parkinson's disease and schizophrenia. Extensive studies have focused on the regulation of D2R-mediated extracellular-signal-regulated kinase (ERK) 1/2 signaling; however, the manner in which ERKs are activated upon the stimulation of a specific signaling pathway of D2R remains unclear. The present study conducted a variety of experimental techniques, including loss-of-function experiments, site-directed mutagenesis, and the determination of protein interactions, in order to investigate the mechanisms underlying ß-arrestin-biased signaling-pathway-mediated ERK activation. We found that the stimulation of the D2R ß-arrestin signaling pathway caused Mdm2, an E3 ubiquitin ligase, to move from the nucleus to the cytoplasm and interact with tyrosine phosphorylated G-protein-coupled receptor kinase 2 (GRK2), which was facilitated by Src, a non-receptor tyrosine kinase. This interaction led to the ubiquitination of GRK2, which then moved to the plasma membrane and interacted with activated D2R, followed by the phosphorylation of D2R as well as the mediation of ERK activation. In conclusion, Mdm2-mediated GRK2 ubiquitination, which is selectively triggered by the stimulation of the D2R ß-arrestin signaling pathway, is necessary for GRK2 membrane translocation and its interaction with D2R, which in turn mediates downstream ERK signaling. This study is primarily novel and provides essential information with which to better understand the detailed mechanisms of D2R-dependent signaling.


Assuntos
Quinase 2 de Receptor Acoplado a Proteína G , Transdução de Sinais , beta-Arrestinas/metabolismo , Quinase 2 de Receptor Acoplado a Proteína G/genética , Quinase 2 de Receptor Acoplado a Proteína G/metabolismo , Transdução de Sinais/fisiologia , beta-Arrestina 1/metabolismo , Receptores de Dopamina D2/genética , Receptores de Dopamina D2/metabolismo , Fosforilação/fisiologia , Dopamina , Ubiquitinação
4.
Sheng Li Xue Bao ; 75(5): 703-713, 2023 Oct 25.
Artigo em Chinês | MEDLINE | ID: mdl-37909141

RESUMO

Hyperhomocysteinemia (HHcy) is considered to be an independent risk factor for cardiovascular diseases, but the molecular mechanisms underlying its pathogenesis are not fully understood. Endothelial dysfunction is a key initiating factor in the pathogenesis of atherosclerosis, which is commonly observed in almost all HHcy-induced vascular diseases. HHcy promotes oxidative stress, inhibits nitric oxide production, suppresses hydrogen sulfide signaling pathway, promotes endothelial mesenchymal transition, activates coagulation pathways, and promotes protein N-homocysteination and cellular hypomethylation, all of which can cause endothelial dysfunction. This article reviews the specific links between HHcy and endothelial dysfunction, and highlights recent evidence that endothelial mesenchymal transition contributes to HHcy-induced vascular damage, with a hope to provide new ideas for the clinical treatment of HHcy-related vascular diseases.


Assuntos
Aterosclerose , Doenças Cardiovasculares , Hiper-Homocisteinemia , Humanos , Endotélio Vascular , Homocisteína/metabolismo , Hiper-Homocisteinemia/complicações , Estresse Oxidativo , Fatores de Risco
5.
Angew Chem Int Ed Engl ; 62(29): e202303242, 2023 Jul 17.
Artigo em Inglês | MEDLINE | ID: mdl-37142555

RESUMO

The construction of nanotubular structures with non-deformable inner pores is of both fundamental and practical significance. Herein we report a strategy for creating molecular nanotubes with defined lengths. Macrocyclic (MC) units based on shape-persistent hexakis(m-phenylene ethynylene) (m-PE) macrocycle MC-1, which are known to stack into hydrogen-bonded tubular assemblies, are tethered by oligo(ß-alanine) linkers to give tubular stacks MC-2 and MC-4 that have two and four MC units, respectively. The covalently linked MC units in MC-2 and MC-4 undergo face-to-face stacking through intramolecular non-covalent interactions that further results in the helical stacks of these compounds. Oligomer MC-4 can form potassium and proton channels across lipid bilayers, with the channels being open continuously for over 60 seconds, which is among the longest open durations for synthetic ion channels and indicates that the thermodynamic stability of the self-assembling channels can be drastically enhanced by reducing the number of molecular components involved. This study demonstrates that covalently tethering shape-persistent macrocyclic units is a feasible and reliable approach for building molecular nanotubes that otherwise are difficult to create de novo. The extraordinarily long lifetimes of the ion channels formed by MC-2 and MC-4 suggest the likelihood of constructing the next-generation synthetic ion channels with unprecedented stability.

6.
Biochem Biophys Res Commun ; 628: 40-48, 2022 11 05.
Artigo em Inglês | MEDLINE | ID: mdl-36063601

RESUMO

Dopamine D2 receptor (D2R) plays a key role in the regulation of glucose homeostasis by stimulating the secretion of many glucoregulatory hormones. Insulin resistance (IR) is associated with the pathogenesis of metabolic disorders which occurs when PI3K/Akt signaling pathway is downregulated. However, the potential involvement of D2R in insulin resistance remains unclear. In the present study, we investigated the regulation of glucose transport by D2-like receptors and discovered that activation of D2R, but not D3R or D4R, suppressed insulin-induced 2-DOG uptake and Glut4 membrane translocation in a GRK2- and Src-dependent manner. Further study revealed that activation of D2R inhibits insulin-induced phosphorylation of Akt at Thr308 and Ser473, which are hallmarks of its kinase activity, by increasing the interaction of tyrosine phosphorylated GRK2 with Akt and then preventing Akt from interacting with PDK1. Thus, this study demonstrates that Src mediated GRK2 tyrosine phosphorylation is an essential physiological event that mediates the roles of D2R in insulin resistance.


Assuntos
Quinase 2 de Receptor Acoplado a Proteína G , Resistência à Insulina , Receptores de Dopamina D2 , Animais , Dopamina , Quinase 2 de Receptor Acoplado a Proteína G/metabolismo , Glucose/metabolismo , Humanos , Insulina/metabolismo , Resistência à Insulina/genética , Resistência à Insulina/fisiologia , Camundongos , Fosfatidilinositol 3-Quinases/metabolismo , Fosforilação , Proteínas Proto-Oncogênicas c-akt/metabolismo , Receptores de Dopamina D2/metabolismo , Tirosina/metabolismo
7.
Bioorg Med Chem ; 63: 116729, 2022 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-35439688

RESUMO

In this article, we report the discovery of a series of pyrimidopyridones as inhibitors of IRAK4 kinase. From a previously disclosed 5-azaquinazoline series, we found that switching the pyridine ring for an N-substituted pyridone gave a novel hinge binding scaffold which retained potency against IRAK4. Importantly, introduction of the carbonyl established an internal hydrogen bond with the 4-NH, establishing a conformational lock and allowing truncation of the large basic substituent to a 1-methylcyclopyl group. Subsequent optimisation, facilitated by X-ray crystal structures, allowed identification of preferred substituents at both the pyridone core and pyrazole. Subsequent combinations of optimal groups allowed control of lipophilicity and identification of potent and selective inhibitors of IRAK4 with better in vitro permeability and lower clearance.


Assuntos
Quinases Associadas a Receptores de Interleucina-1 , Piridonas , Conformação Molecular , Piridonas/farmacologia , Relação Estrutura-Atividade
8.
Bioorg Chem ; 116: 105299, 2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-34454300

RESUMO

The development of cationic polymers as non-viral gene vectors has been hurdled by their high toxicity, thus degradable and biocompatible polymers are urgently demanded. Herein, five polyesters (B3a-B3e) were synthesized based on the ring-opening copolymerization between α-allyl-δ-valerolactone and δ-valerolactone derivatives decorated with alkyl or alkoxyl chains of different lengths, followed by the modification with 1,5,9-triazacyclododecyl ([12]aneN3) through thiol-ene click reactions. The five polyesters effectively condensed DNA into nanoparticles. Of them, B3a with a shorter alkyl chain and B3d with more positive charged units showed stronger DNA condensing performance and can completely retard the migration of DNA at N/P = 1.6 in the presence of DOPE. B3b/DOPE with a longer alkyl chain exhibited the highest transfection efficiency in HeLa cells with 1.8 times of 25 kDa PEI, while B3d/DOPE with more positive charged units exhibited highest transfection efficiency in A549 cells with 2.3 times of 25 kDa PEI. B3b/DOPE and B3d/DOPE successfully delivered pEGFP into zebrafish, which was superior to 25 kDa PEI (1.5 folds and 1.1 folds, respectively). The cytotoxicity measurements proved that the biocompatibility of these polyesters was better than 25 kDa PEI, due to their degradable property in acid environment. The results indicated that these cationic polyesters can be developed as potential non-viral gene vectors for DNA delivery.


Assuntos
DNA/genética , Técnicas de Transferência de Genes , Lactonas/química , Nanopartículas/química , Poliésteres/química , Cátions/química , Cátions/farmacologia , Linhagem Celular Tumoral , Sobrevivência Celular/efeitos dos fármacos , Relação Dose-Resposta a Droga , Vetores Genéticos/química , Humanos , Estrutura Molecular , Plasmídeos/genética , Poliésteres/farmacologia , Polimerização , Relação Estrutura-Atividade
9.
BMC Genomics ; 18(1): 42, 2017 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-28061745

RESUMO

BACKGROUND: Sunflower Verticillium wilt (SVW) is a vascular disease caused by root infection with Verticillium dahliae (V. dahlia). It is a serious threat to the yield and quality of sunflower. However, chemical and agronomic measures for controlling this disease are not effective. The selection of more resistant genotypes is a desirable strategy to reduce contamination. A deeper knowledge of the molecular mechanisms and genetic basis underlying sunflower Verticillium wilt is necessary to accelerate breeding progress. RESULTS: An RNA-Seq approach was used to perform global transcriptome profiling on the roots of resistant (S18) and susceptible (P77) sunflower genotypes infected with V. dahlia. Different pairwise transcriptome comparisons were examined over a time course (6, 12 and 24 h, and 2, 3, 5 and 10 d post inoculation). In RD, SD and D datasets, 1231 genes were associated with SVW resistance in a genotype-common transcriptional pattern. Moreover, 759 and 511 genes were directly related to SVW resistance in the resistant and susceptible genotypes, respectively, in a genotype-specific transcriptional pattern. Most of the genes were demonstrated to participate in plant defense responses; these genes included peroxidase (POD), glutathione peroxidase, aquaporin PIP, chitinase, L-ascorbate oxidase, and LRR receptors. For the up-regulated genotype-specific differentially expressed genes (DEGs) in the resistant genotype, higher average fold-changes were observed in the resistant genotype compared to those in the susceptible genotype. An inverse effect was observed in the down-regulated genotype-specific DEGs in the resistant genotype. KEGG analyses showed that 98, 112 and 52 genes were classified into plant hormone signal transduction, plant-pathogen interaction and flavonoid biosynthesis categories, respectively. Many of these genes, such as CNGC, RBOH, FLS2, JAZ, MYC2 NPR1 and TGA, regulate crucial points in defense-related pathway and may contribute to V. dahliae resistance in sunflower. CONCLUSIONS: The transcriptome profiling results provided a clearer understanding of the transcripts associated with the crosstalk between sunflower and V. dahliae. The results identified several differentially expressed unigenes involved in the hyper sensitive response (HR) and the salicylic acid (SA)/jasmonic acid (JA)-mediated signal transduction pathway for resistance against V. dahliae. These results are useful for screening resistant sunflower genotypes.


Assuntos
Perfilação da Expressão Gênica , Helianthus/genética , Helianthus/microbiologia , Verticillium/fisiologia , Genes de Plantas/genética , Genótipo , Helianthus/fisiologia , Doenças das Plantas/microbiologia , Raízes de Plantas/genética , Transcrição Gênica
10.
Genomics ; 107(1): 9-15, 2016 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-26697761

RESUMO

Non-coding RNA (ncRNA) genes make transcripts as same as the encoding genes, and ncRNAs directly function as RNAs rather than serve as blueprints for proteins. As the function of ncRNA is closely related to organelle genomes, it is desirable to explore ncRNA function by confirming its provenance. In this paper, the topology secondary structure, motif and the triplets under three reading frames are considered as parameters of ncRNAs. A method of SVM combining the increment of diversity (ID) algorithm is applied to construct the classifier. When the method is applied to the ncRNA dataset less than 80% sequence identity, the overall accuracies reach 95.57%, 96.40% in the five-fold cross-validation and the jackknife test, respectively. Further, for the independent testing dataset, the average prediction success rate of our method achieved 93.24%. The higher predictive success rates indicate that our method is very helpful for distinguishing ncRNAs from various organelle genomes.


Assuntos
Algoritmos , DNA de Cloroplastos/química , DNA de Cinetoplasto/química , DNA Mitocondrial/química , Fases de Leitura Aberta , RNA não Traduzido/química , Sequência de Bases , DNA de Cloroplastos/genética , DNA de Cinetoplasto/genética , DNA Mitocondrial/genética , Conformação de Ácido Nucleico , RNA não Traduzido/genética , Análise de Sequência de DNA/métodos
11.
FEBS Lett ; 598(4): 400-414, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38302840

RESUMO

The insulin and dopaminergic systems in the brain are associated with schizophrenia and Parkinson's disease with respect to etiology and treatment. The present study investigated the crosstalk between the insulin receptor (IR) and dopamine receptor and found that insulin stimulation selectively inhibits signaling of D3 R in a PKCßII-dependent manner. Upon insulin stimulation, E3 ligase enzyme Mdm2 moves out of the nucleus to ubiquitinate PKCßII. Subsequently, ubiquitinated PKCßII translocates to the cell membrane and interacts with D3 R in a phosphorylation-dependent manner at S229/257, resulting in the attenuation of D3 R signaling and initiating clathrin-mediated endocytosis and downregulation. Considering that both IR and D3 R are closely related to some neuropsychosis, this study could provide new molecular insight into the etiology of the disorder.


Assuntos
Dopamina , Insulinas , Proteína Quinase C beta , Ubiquitinação , Transdução de Sinais , Ubiquitina/metabolismo , Insulinas/metabolismo
12.
iScience ; 27(3): 109045, 2024 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-38361622

RESUMO

Splenectomy often accompanies distal pancreatectomy for pancreatic cancer. However, debates persist on splenic function loss impact. Prior studies in mice revealed splenectomy promotes pancreatic cancer growth by altering CD4/Foxp3 and CD8/Foxp3 ratios. The effect on other immune cells remains unclear. Clinical observations indicate splenectomy induces immunosuppression, heightening recurrence and metastasis risk. Here, we established an orthotopic pancreatic cancer model with splenectomy and observed a significant increase in tumor burden. Flow cytometry revealed elevated MDSCs, CD8+PD-1high+ T cells, and reduced CD4+ T cells, CD8+ T cells, and natural killer cells in tumors. Bulk sequencing identified increased MicroRNA (miRNA) hsa-7b-5p post-splenectomy, correlating with staging and immunosuppression. Similar results were obtained in vivo by constructing a KPC-miRNA hsa-7b-5p-sh cell line. These findings suggest that splenectomy enhances the expression of miRNA hsa-7b-5p, inhibits the tumor immune microenvironment, and promotes pancreatic cancer growth.

13.
Spectrochim Acta A Mol Biomol Spectrosc ; 318: 124501, 2024 Oct 05.
Artigo em Inglês | MEDLINE | ID: mdl-38796888

RESUMO

A simple benzopyran-based fluorescence probe DCA-Apa detection of volatile amine has been synthesized. DCA-Apa can recognize volatile amines by dual channel mode (changing from blue to light yellow in sunlight, and from weak pink to orange under 365 nm) in pure water system. DCA-Apa has the advantages of ultra-fast response (∼6 s), NIR emission (655 nm), and a good fluorescence response for many amines. The sensing label or gel loaded with DCA-Apa was prepared by the dipping or mixing method using filter paper or gelatin as solid carriers, which can identify volatile amine vapor and monitor the freshness of salmon by colorimetric and fluorescent dual channels. When the color of the label changes to light yellow-green or the fluorescence of the label becomes orange fluorescence (365 nm UV lamp), it indicates that the fish has rotted. The two-channel method makes up for the deficiency of the single colorimetric method, and establishes a theoretical foundation for more precise assessment of fish freshness.


Assuntos
Aminas , Corantes Fluorescentes , Espectrometria de Fluorescência , Animais , Corantes Fluorescentes/química , Aminas/química , Aminas/análise , Espectrometria de Fluorescência/métodos , Peixes , Compostos Orgânicos Voláteis/análise , Géis/química , Salmão , Colorimetria/métodos
14.
J Hazard Mater ; 469: 134003, 2024 May 05.
Artigo em Inglês | MEDLINE | ID: mdl-38492394

RESUMO

In this study, we have effectively prepared a novel fluorescent probe named HDXM based on benzopyran derivatives for the ultrafast detection (within 3 s) of SO2 derivatives or biogenic amines. HDXM showed a noticeable color change after the addition of SO2 derivatives (from purple to colorless) or biogenic amines (from purple to blue), indicating that HDXM can identify two analytes with the naked eye. It is worth noting that HDXM can be used to detect SO2 derivatives in actual sugar samples, and to image HSO3-/SO32- in living cells. More importantly, sensing labels (HDXM-loaded filter paper or agarose hydrogel) enable real-time visual monitoring of salmon freshness through colorimetric and fluorescence dual channels. Compared with the Chinese national standard method, the sensing label is an effective tool for evaluating the freshness of fish. Benefiting from its excellent solubility and fluorescence performance, HDXM can be used as a versatile fluorescent material in various applications, including flexible films, glass coatings, impregnating dyes, printing, and fingerprint ink. HDXM is expected to be a promising and valuable multifunctional tool for food safety and fluorescent materials.


Assuntos
Aminas Biogênicas , Corantes Fluorescentes , Animais , Fluorescência , Alimentos Marinhos/análise , Carboidratos , Peixes
15.
Talanta ; 274: 126120, 2024 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-38640603

RESUMO

Peroxynitrite (ONOO-) and cell plasma membrane (CPM) are two key factors in cell pyroptosis during the progression of abdominal aortic aneurysm (AAA). However, their combined temporal and spatial roles in initiating AAA pathogenesis remain unclear. Herein, we developed a two-photon fluorescence probe, BH-Vis, enabling real-time dynamic detection of CPM and ONOO- changes, and revealing their interplay in AAA. BH-Vis precisely targets CPM with reduced red fluorescence intensity correlating with diminished CPM tension. Concurrently, a blue shift of the fluorescence signal of BH-Vis occurs in response to ONOO- offering a reliable ratiometric detection mode with enhanced accuracy by minimizing external testing variables. More importantly, two photon confocal imaging with palmitic acid (PA) and ganglioside (GM1) manipulation, which modulating cell pyroptosis, showcases reliable fluorescence fluctuations. This groundbreaking application of BH-Vis in a mouse AAA model demonstrates its significant potential for accurately identifying cell pyroptosis levels during AAA development.


Assuntos
Aneurisma da Aorta Abdominal , Membrana Celular , Imagem Óptica , Ácido Peroxinitroso , Aneurisma da Aorta Abdominal/metabolismo , Aneurisma da Aorta Abdominal/diagnóstico por imagem , Aneurisma da Aorta Abdominal/patologia , Ácido Peroxinitroso/metabolismo , Animais , Camundongos , Membrana Celular/metabolismo , Membrana Celular/química , Humanos , Corantes Fluorescentes/química , Piroptose/efeitos dos fármacos , Camundongos Endogâmicos C57BL , Masculino , Fótons
16.
Epigenomics ; 15(15): 769-795, 2023 08.
Artigo em Inglês | MEDLINE | ID: mdl-37718931

RESUMO

Homocysteine has a wide range of biological effects. However, the specific molecular mechanism of its pathogenicity is still unclear. The diseases induced by hyperhomocysteinemia (HHcy) are called homocysteine-related diseases. Clinical treatment of HHcy is mainly through folic acid and B-complex vitamins, which are not effective in reducing the associated end point events. Epigenetics is the alteration of heritable genes caused by DNA methylation, histone modification, noncoding RNAs and chromatin remodeling without altering the DNA sequence. In recent years the role of epigenetics in homocysteine-associated diseases has been gradually discovered. This article summarizes the latest evidence on the role of epigenetics in HHcy, providing new directions for its prevention and treatment.


Assuntos
Metilação de DNA , Epigênese Genética , Humanos , Epigenômica , Montagem e Desmontagem da Cromatina , Homocisteína
17.
Comput Biol Med ; 157: 106711, 2023 05.
Artigo em Inglês | MEDLINE | ID: mdl-36924738

RESUMO

Long non-coding RNAs (lncRNAs) play important roles by regulating proteins in many biological processes and life activities. To uncover molecular mechanisms of lncRNA, it is very necessary to identify interactions of lncRNA with proteins. Recently, some machine learning methods were proposed to detect lncRNA-protein interactions according to the distribution of known interactions. The performances of these methods were largely dependent upon: (1) how exactly the distribution of known interactions was characterized by feature space; (2) how discriminative the feature space was for distinguishing lncRNA-protein interactions. Because the known interactions may be multiple and complex model, it remains a challenge to construct discriminative feature space for lncRNA-protein interactions. To resolve this problem, a novel method named DFRPI was developed based on deep autoencoder and marginal fisher analysis in this paper. Firstly, some initial features of lncRNA-protein interactions were extracted from the primary sequences and secondary structures of lncRNA and protein. Secondly, a deep autoencoder was exploited to learn encode parameters of the initial features to describe the known interactions precisely. Next, the marginal fisher analysis was employed to optimize the encode parameters of features to characterize a discriminative feature space of the lncRNA-protein interactions. Finally, a random forest-based predictor was trained on the discriminative feature space to detect lncRNA-protein interactions. Verified by a series of experiments, the results showed that our predictor achieved the precision of 0.920, recall of 0.916, accuracy of 0.918, MCC of 0.836, specificity of 0.920, sensitivity of 0.916 and AUC of 0.906 respectively, which outperforms the concerned methods for predicting lncRNA-protein interaction. It may be suggested that the proposed method can generate a reasonable and effective feature space for distinguishing lncRNA-protein interactions accurately. The code and data are available on https://github.com/D0ub1e-D/DFRPI.


Assuntos
RNA Longo não Codificante , RNA Longo não Codificante/genética , Algoritmos , Aprendizado de Máquina , Biologia Computacional/métodos
18.
Front Pharmacol ; 14: 1111320, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36843938

RESUMO

Myocardial remodeling refers to structural and functional disorders of the heart caused by molecular biological changes in the cardiac myocytes in response to neurological and humoral factors. A variety of heart diseases, such as hypertension, coronary artery disease, arrhythmia, and valvular heart disease, can cause myocardial remodeling and eventually lead to heart failure. Therefore, counteracting myocardial remodeling is essential for the prevention and treatment of heart failure. Sirt1 is a nicotinamide adenine dinucleotide+-dependent deacetylase that plays a wide range of roles in transcriptional regulation, energy metabolism regulation, cell survival, DNA repair, inflammation, and circadian regulation. It positively or negatively regulates myocardial remodeling by participating in oxidative stress, apoptosis, autophagy, inflammation, and other processes. Taking into account the close relationship between myocardial remodeling and heart failure and the involvement of SIRT1 in the development of the former, the role of SIRT1 in the prevention of heart failure via inhibition of myocardial remodeling has received considerable attention. Recently, multiple studies have been conducted to provide a better understanding of how SIRT1 regulates these phenomena. This review presents the progress of research involving SIRT1 pathway involvement in the pathophysiological mechanisms of myocardial remodeling and heart failure.

19.
Front Microbiol ; 14: 1200678, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37250059

RESUMO

Promoters are the basic functional cis-elements to which RNA polymerase binds to initiate the process of gene transcription. Comprehensive understanding gene expression and regulation depends on the precise identification of promoters, as they are the most important component of gene expression. This study aimed to develop a machine learning-based model to predict promoters in Klebsiella aerogenes (K. aerogenes). In the prediction model, the promoter sequences in K. aerogenes genome were encoded by pseudo k-tuple nucleotide composition (PseKNC) and position-correlation scoring function (PCSF). Numerical features were obtained and then optimized using mRMR by combining with support vector machine (SVM) and 5-fold cross-validation (CV). Subsequently, these optimized features were inputted into SVM-based classifier to discriminate promoter sequences from non-promoter sequences in K. aerogenes. Results of 10-fold CV showed that the model could yield the overall accuracy of 96.0% and the area under the ROC curve (AUC) of 0.990. We hope that this model will provide help for the study of promoter and gene regulation in K. aerogenes.

20.
FEBS J ; 290(21): 5204-5233, 2023 11.
Artigo em Inglês | MEDLINE | ID: mdl-37531324

RESUMO

Dopamine D2 receptor (D2 R) has been shown to activate extracellular signal-regulated kinases (ERKs) via distinct pathways dependent on either G-protein or ß-arrestin. However, there has not been a systematic study of the regulatory process of D2 R-mediated ERKs activation by G protein- versus ß-arrestin-dependent signaling since D2 R stimulation of ERKs reflects the simultaneous action of both pathways. Here, we investigated that differential regulation of D2 R-mediated ERKs activation via these two pathways. Our results showed that G protein-dependent ERKs activation was transient, rapid, reached maximum level at around 2 min, and importantly, the activated ERKs were entirely confined to the cytoplasm. In contrast, ß-arrestin-dependent ERKs activation was more sustained, slower, reached maximum level at around 10 min, and phosphorylated ERKs translocated into the nucleus. Src was found to be commonly involved in both the G protein- and ß-arrestin-dependent pathway-mediated ERKs activation. Pertussis toxin Gi/o inhibitor, GRK2-CT, AG1478 epidermal growth factor receptor inhibitor, and wortmannin phosphoinositide 3-kinase inhibitor all blocked G protein-dependent ERKs activation. In contrast, GRK2 and ß-Arr2 played a main role in ß-arrestin-dependent ERKs activation. Receptor endocytosis showed minimal effect on the activation of ERKs mediated by both pathways. Furthermore, we found that the formation of a complex composed of phospho-ERKs, ß-Arr2, and importinß1 promoted the nuclear translocation of activated ERKs. The differential regulation of various cellular components, as well as temporal and spatial patterns of ERKs activation via these two pathways, suggest the existence of distinct physiological outcomes.


Assuntos
Dopamina , MAP Quinases Reguladas por Sinal Extracelular , Arrestinas/genética , beta-Arrestinas , Dopamina/farmacologia , Proteínas de Ligação ao GTP/metabolismo , Fosfatidilinositol 3-Quinases/genética , Fosfatidilinositol 3-Quinases/metabolismo , Receptores Dopaminérgicos/metabolismo
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