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1.
Anticancer Res ; 40(1): 535-543, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31892609

RESUMO

BACKGROUND/AIM: To assess the impact of vitamin D supplementation on genomic and metabolomic profiles and relate them to the individual's responsiveness to varying doses of vitamin D3 Patients and Methods: Healthy adults were given either 600, 4000 or 10,000 IUs vitamin D3/day for 6 months. Circulating parathyroid hormone (PTH), 25-hydroxyvitamin D [25(OH)D], calcium, peripheral white blood cells broad gene expression and urine and serum metabolomic profiles were evaluated. RESULTS: There was a dose-dependent effect of vitamin D supplementation on serum 25(OH)D, PTH and broad gene expression. Serum calcium levels remained normal for all study subjects and no untoward toxicity was observed. The metabolomic profiles were related to the genomic expression analysis. There were significant inter-individual effects on gene expression and metabolomic profile in response to the same dose of vitamin D3 supplementation, despite similar changes in 25(OH)D and PTH concentrations. CONCLUSION: These results may help explain the variability observed in clinical trials regarding vitamin D's non-calcemic health benefits.


Assuntos
Suplementos Nutricionais , Genômica , Metabolômica , Vitamina D/farmacologia , Adulto , Relação Dose-Resposta a Droga , Feminino , Regulação da Expressão Gênica/efeitos dos fármacos , Humanos , Masculino , Hormônio Paratireóideo/sangue , Análise de Componente Principal , Mapas de Interação de Proteínas/efeitos dos fármacos , Vitamina D/análogos & derivados , Vitamina D/sangue
2.
J Pharm Biomed Anal ; 177: 112732, 2020 Jan 05.
Artigo em Inglês | MEDLINE | ID: mdl-31568965

RESUMO

Dingkun Dan (DKD) has been widely used for a variety of gynecological disease. However, the systematic analysis of the chemical constituents of DKD has not been well established because of the complexity of the formula and confidentiality. In this paper, liquid chromatography Q Exactive high resolution accurate mass spectrometry (UHPLC-QE-HRMS) with automated MetaboLynx analysis was established to characterize the chemical constituents of DKD. The analysis was performed on a Water Acquity UPLC® HSS T3 using a gradient elution system. Full scan ranged 100-1500 m/z in positive and negative ion mode combined with MS/MS fragmentation for top 5 ions was proposed for aiding the structural identification of the components. All of the peaks were tentatively characterized by not only comparing the retention time and MS data with those from reported literature and database, but also summarizing the fragmentation pathways and promoting to other ingredients identification. Additionally, the network pharmacology study had been used to analysis the identified ingredients and DKD's clinical diseases. In this work, a total of 121 components and isomers were characterized, including amino acids, phenolic acids, lactones, terpenoids, alkaloids, saponins, flavonoids, and other compounds. Network pharmacology analysis showed that identified compounds, such as ginsenosides and notoginsenosides, crocin I, echinacoside, rutin and verbascoside, could be responsible for the pharmacological activity of DKD by regulating the hormone with related metabolism pathways, estrogen signaling pathways and serotonergic synapse pathways. It could indicate that UHPLC-MS showed obvious superiority used to find the potential bioactive compounds of complicated TCM formula without the process of extraction and isolation.


Assuntos
Medicamentos de Ervas Chinesas/análise , Controle de Qualidade , Cromatografia Líquida de Alta Pressão/métodos , Simulação por Computador , Medicamentos de Ervas Chinesas/química , Medicamentos de Ervas Chinesas/farmacologia , Medicamentos de Ervas Chinesas/uso terapêutico , Feminino , Doenças dos Genitais Femininos/tratamento farmacológico , Doenças dos Genitais Femininos/metabolismo , Humanos , Simulação de Acoplamento Molecular , Mapas de Interação de Proteínas/efeitos dos fármacos , Transdução de Sinais/efeitos dos fármacos , Espectrometria de Massas em Tandem/métodos
3.
Medicine (Baltimore) ; 98(38): e17267, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31568004

RESUMO

Smoking is a substantial risk factor for many respiratory diseases. This study aimed to identify the gene and microRNA changes related to smoking in human airway epithelium by bioinformatics analysis.From the Gene Expression Omnibus (GEO) database, the mRNA datasets GSE11906, GSE22047, GSE63127, and microRNA dataset GSE14634 were downloaded, and were analyzed using GEO2R. Functional enrichment analysis of the differentially expressed genes (DEGs) was enforced using DAVID. The protein-protein interaction (PPI) network and differentially expressed miRNAs (DEMs)- DEGs network were executed by Cytoscape.In total, 107 DEGs and 10 DEMs were determined. Gene Ontology (GO) analysis revealed that DEGs principally enriched in oxidation-reduction process, extracellular space and oxidoreductase activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway demonstrated that DEGs were principally enriched in metabolism of xenobiotics by cytochrome P450 and chemical carcinogenesis. The PPI network revealed 15 hub genes, including NQO1, CYP1B1, AKR1C1, CYP1A1, AKR1C3, CEACAM5, MUCL1, B3GNT6, MUC5AC, MUC12, PTGER4, CALCA, CBR1, TXNRD1, and CBR3. Cluster analysis showed that these hub genes were associated with adenocarcinoma in situ, squamous cell carcinoma, cell differentiation, inflammatory response, oxidative DNA damage, oxidative stress response and tumor necrosis factor. Hsa-miR-627-5p might have the most target genes, including ITLN1, TIMP3, PPP4R4, SLC1A2, NOVA1, RNFT2, CLDN10, TMCC3, EPHA7, SRPX2, PPP1R16B, GRM1, HS3ST3A1, SFRP2, SLC7A11, and KLHDC8A.We identified several molecular changes induced by smoking in human airway epithelium. This study may provide some candidate genes and microRNAs for assessing the risk of lung diseases caused by smoking.


Assuntos
Expressão Gênica/efeitos dos fármacos , MicroRNAs/metabolismo , Mucosa Respiratória/metabolismo , Fumar/efeitos adversos , Regulação da Expressão Gênica/efeitos dos fármacos , Humanos , Mapas de Interação de Proteínas/efeitos dos fármacos , Mucosa Respiratória/efeitos dos fármacos , Fumar/metabolismo
4.
Nat Commun ; 10(1): 4521, 2019 10 04.
Artigo em Inglês | MEDLINE | ID: mdl-31586061

RESUMO

Designing highly specific modulators of protein-protein interactions (PPIs) is especially challenging in the context of multiple paralogs and conserved interaction surfaces. In this case, direct generation of selective and competitive inhibitors is hindered by high similarity within the evolutionary-related protein interfaces. We report here a strategy that uses a semi-rational approach to separate the modulator design into two functional parts. We first achieve specificity toward a region outside of the interface by using phage display selection coupled with molecular and cellular validation. Highly selective competition is then generated by appending the more degenerate interaction peptide to contact the target interface. We apply this approach to specifically bind a single PDZ domain within the postsynaptic protein PSD-95 over highly similar PDZ domains in PSD-93, SAP-97 and SAP-102. Our work provides a paralog-selective and domain specific inhibitor of PSD-95, and describes a method to efficiently target other conserved PPI modules.


Assuntos
Anticorpos/química , Domínios PDZ , Peptídeos/química , Engenharia de Proteínas , Mapas de Interação de Proteínas/efeitos dos fármacos , Animais , Anticorpos/farmacologia , Células COS , Proteína 4 Homóloga a Disks-Large/antagonistas & inibidores , Proteína 4 Homóloga a Disks-Large/metabolismo , Desenho de Drogas , Mapeamento de Epitopos , Modelos Moleculares , Biblioteca de Peptídeos , Peptídeos/farmacologia , Ligação Proteica , Proteínas Recombinantes/metabolismo
5.
Cell Physiol Biochem ; 53(4): 731-745, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31613064

RESUMO

BACKGROUND/AIMS: 3-Deazaneplanocin, DZNep, has been reported to inhibit the EZH2 histone methylase and to induce cell apoptosis in chondrosarcomas (CS). The present study aims to confirm the therapeutic potential of EZH2 inhibitors and investigate the molecular mechanisms of DZNep in chondrosarcomas. METHODS: CS cell lines and primary cultures were used. Apoptosis was investigated using PARP cleavage, caspase 3/7 activity, or Apo2.7 expression. S-adenosylhomocysteine (SAH) and S-adenosylmethionine (SAM) were quantified by UHPLC-MS/MS. Differentially expressed genes in treated-chondrosarcomas and chondrocytes were researched by microarray analysis. RESULTS: DZNep induced apoptosis in chondrosarcomas both in vivo and in vitro. However, this effect was not correlated to EZH2 expression nor activity, and EZH2 knock-down by siRNA did not reduce CS viability. Additionally, the reduction of H3K27me3 induced by GSK126 or tazemetostat (EPZ-6438) did not provoke chondrosarcoma death. However, as expected, DZNep induced SAH accumulation and reduced SAM:SAH ratio. Further, microarray analysis suggests a key role of EGFR in antitumoral effect of DZNep, and pharmacological inhibition of EGFR reduced chondrosarcoma survival. CONCLUSION: EZH2 is not an adequate target for chondrosarcoma treatment. However, DZNep induces apoptosis in chondrosarcomas in vitro and in vivo, by a mechanism likely mediated though EGFR expression. Consequently, it would be worth initiating clinical trials to evaluating efficiency to S-adenosylhomocysteine hydrolase or EGFR inhibitors in patients with chondrosarcomas.


Assuntos
Adenosina/análogos & derivados , Regulação para Baixo/efeitos dos fármacos , Proteína Potenciadora do Homólogo 2 de Zeste/metabolismo , Adenosina/farmacologia , Animais , Apoptose/efeitos dos fármacos , Neoplasias Ósseas/metabolismo , Neoplasias Ósseas/patologia , Linhagem Celular Tumoral , Sobrevivência Celular/efeitos dos fármacos , Condrossarcoma/metabolismo , Condrossarcoma/patologia , Dano ao DNA/efeitos dos fármacos , Proteína Potenciadora do Homólogo 2 de Zeste/antagonistas & inibidores , Proteína Potenciadora do Homólogo 2 de Zeste/genética , Receptores ErbB/genética , Receptores ErbB/metabolismo , Histonas/metabolismo , Humanos , Masculino , Camundongos , Camundongos Nus , Mapas de Interação de Proteínas/efeitos dos fármacos , Interferência de RNA , RNA Interferente Pequeno/metabolismo , S-Adenosil-Homocisteína/metabolismo
6.
World J Gastroenterol ; 25(33): 4921-4932, 2019 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-31543683

RESUMO

BACKGROUND: The potential role of chronic inflammation in the development of cancer has been widely recognized. However, there has been little research fully and thoroughly exploring the molecular link between hepatitis B virus (HBV) and hepatocellular carcinoma (HCC). AIM: To elucidate the molecular links between HBV and HCC through analyzing the molecular processes of HBV-HCC using a multidimensional approach. METHODS: First, maladjusted genes shared between HBV and HCC were identified by disease-related differentially expressed genes. Second, the protein-protein interaction network based on dysfunctional genes identified a series of dysfunctional modules and significant crosstalk between modules based on the hypergeometric test. In addition, key regulators were detected by pivot analysis. Finally, targeted drugs that have regulatory effects on diseases were predicted by modular methods and drug target information. RESULTS: The study found that 67 genes continued to increase in the HBV-HCC process. Moreover, 366 overlapping genes in the module network participated in multiple functional blocks. It could be presumed that these genes and their interactions play an important role in the relationship between inflammation and cancer. Correspondingly, significant crosstalk constructed a module level bridge for HBV-HCC molecular processes. On the other hand, a series of non-coding RNAs and transcription factors that have potential pivot regulatory effects on HBV and HCC were identified. Among them, some of the regulators also had persistent disorders in the process of HBV-HCC including microRNA-192, microRNA-215, and microRNA-874, and early growth response 2, FOS, and Kruppel-like factor 4. Therefore, the study concluded that these pivots are the key bridge molecules outside the module. Last but not least, a variety of drugs that may have some potential pharmacological or toxic side effects on HBV-induced HCC were predicted, but their mechanisms still need to be further explored. CONCLUSION: The results suggest that the persistent inflammatory environment of HBV can be utilized as an important risk factor to induce the occurrence of HCC, which is supported by molecular evidence.


Assuntos
Carcinoma Hepatocelular/etiologia , Vírus da Hepatite B/imunologia , Hepatite B Crônica/imunologia , Interações Hospedeiro-Patógeno/genética , Neoplasias Hepáticas/etiologia , Carcinoma Hepatocelular/tratamento farmacológico , Carcinoma Hepatocelular/epidemiologia , Conjuntos de Dados como Assunto , Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Regulação Neoplásica da Expressão Gênica/imunologia , Redes Reguladoras de Genes/efeitos dos fármacos , Redes Reguladoras de Genes/imunologia , Hepatite B Crônica/patologia , Hepatite B Crônica/virologia , Interações Hospedeiro-Patógeno/imunologia , Humanos , Imunoglobulina G/farmacologia , Imunoglobulina G/uso terapêutico , Neoplasias Hepáticas/tratamento farmacológico , Neoplasias Hepáticas/epidemiologia , Melfalan/farmacologia , Melfalan/uso terapêutico , MicroRNAs/antagonistas & inibidores , MicroRNAs/metabolismo , Mapeamento de Interação de Proteínas , Mapas de Interação de Proteínas/efeitos dos fármacos , Mapas de Interação de Proteínas/genética , Mapas de Interação de Proteínas/imunologia , Fatores de Risco , Fatores de Transcrição/antagonistas & inibidores , Fatores de Transcrição/metabolismo
7.
Biomed Pharmacother ; 118: 109253, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31545288

RESUMO

OBJECTIVE: To investigate the regulation mechanism of baicalin on triple negative breast cancer (TNBC)'s biological network by a systematic biological strategy and cytology experiment. METHODS: A systematic biological methodology is utilized to predict the potential targets of baicalin, collect the genes of TNBC, and analyze the TNBC and baicalin's network. After the systematic biological analysis is performed, the cytology experiment, real-time quantitative PCR (qPCR) is used to validate the key biological processes and signaling pathways. RESULTS: After systematic biological analysis, two networks were constructed and analyzed: (1) TNBC network; (2) Baicalin-TNBC protein-protein interaction (PPI) network. Several TNBC-related, treatment-related targets, clusters, signaling pathways and biological processes were found. Cytology experiment shows that baicalin can inhibit the proliferation, migration and invasion of breast cancer MDA-MB-231 cells in vitro (P < 0.05). The results of qPCR showed that baicalin increase the expression of E-cadherin mRNA, and decrease the expression of vimentin, ß-catenin, c-Myc and MMP-7 mRNA in LPS-induced breast cancer MDA-MB-231 cells (P < 0.05). CONCLUSION: Baicalin may achieve anti-tumor effects through regulating the targets, biological processes and pathways found in this research.


Assuntos
Flavonoides/uso terapêutico , Transdução de Sinais , Neoplasias de Mama Triplo Negativas/tratamento farmacológico , Neoplasias de Mama Triplo Negativas/metabolismo , Caderinas/genética , Caderinas/metabolismo , Linhagem Celular Tumoral , Movimento Celular/efeitos dos fármacos , Flavonoides/química , Flavonoides/farmacologia , Humanos , Metaloproteinase 7 da Matriz/genética , Metaloproteinase 7 da Matriz/metabolismo , Invasividade Neoplásica , Mapas de Interação de Proteínas/efeitos dos fármacos , Proteínas Proto-Oncogênicas c-myc/genética , Proteínas Proto-Oncogênicas c-myc/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Transdução de Sinais/efeitos dos fármacos , Vimentina/genética , Vimentina/metabolismo , beta Catenina/genética , beta Catenina/metabolismo
8.
Molecules ; 24(15)2019 Jul 31.
Artigo em Inglês | MEDLINE | ID: mdl-31370197

RESUMO

The interaction between androgen receptor (AR) and coactivator proteins plays a critical role in AR-mediated prostate cancer (PCa) cell growth, thus its inhibition is emerging as a promising strategy for PCa treatment. To develop potent inhibitors of the AR-coactivator interaction, we have designed and synthesized a series of bis-benzamides by modifying functional groups at the N/C-terminus and side chains. A structure-activity relationship study showed that the nitro group at the N-terminus of the bis-benzamide is essential for its biological activity while the C-terminus can have either a methyl ester or a primary carboxamide. Surveying the side chains with various alkyl groups led to the identification of a potent compound 14d that exhibited antiproliferative activity (IC50 value of 16 nM) on PCa cells. In addition, biochemical studies showed that 14d exerts its anticancer activity by inhibiting the AR-PELP1 interaction and AR transactivation.


Assuntos
Benzamidas/farmacologia , Proteínas Correpressoras/química , Neoplasias da Próstata/tratamento farmacológico , Receptores Androgênicos/química , Fatores de Transcrição/química , Antagonistas de Androgênios/química , Antagonistas de Androgênios/farmacologia , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Proteínas Correpressoras/genética , Regulação Neoplásica da Expressão Gênica , Humanos , Masculino , Antígeno Prostático Específico/genética , Neoplasias da Próstata/genética , Neoplasias da Próstata/patologia , Conformação Proteica em alfa-Hélice/efeitos dos fármacos , Mapas de Interação de Proteínas/efeitos dos fármacos , Receptores Androgênicos/efeitos dos fármacos , Relação Estrutura-Atividade , Fatores de Transcrição/genética , Ativação Transcricional/efeitos dos fármacos
9.
Chem Commun (Camb) ; 55(69): 10192-10213, 2019 Aug 22.
Artigo em Inglês | MEDLINE | ID: mdl-31411602

RESUMO

Light is unsurpassed in its ability to modulate biological interactions. Since their discovery, chemists have been fascinated by photosensitive molecules capable of switching between isomeric forms, known as photoswitches. Photoswitchable peptides have been recognized for many years; however, their functional implementation in biological systems has only recently been achieved. Peptides are now acknowledged as excellent protein-protein interaction modulators and have been important in the emergence of photopharmacology. In this review, we briefly explain the different classes of photoswitches and summarize structural studies when they are incorporated into peptides. Importantly, we provide a detailed overview of the rapidly increasing number of examples, where biological modulation is driven by the structural changes. Furthermore, we discuss some of the remaining challenges faced in this field. These exciting proof-of-principle studies highlight the tremendous potential of photocontrollable peptides as optochemical tools for chemical biology and biomedicine.


Assuntos
Descoberta de Drogas , Peptídeos/química , Peptídeos/farmacologia , Sequência de Aminoácidos , Animais , Antibacterianos/química , Antibacterianos/metabolismo , Antibacterianos/farmacologia , Morte Celular/efeitos dos fármacos , Descoberta de Drogas/métodos , Humanos , Isomerismo , Luz , Modelos Moleculares , Ácidos Nucleicos/metabolismo , Peptídeos/metabolismo , Processos Fotoquímicos , Mapas de Interação de Proteínas/efeitos dos fármacos
10.
Nat Commun ; 10(1): 3476, 2019 08 02.
Artigo em Inglês | MEDLINE | ID: mdl-31375661

RESUMO

Recent advances in DNA/RNA sequencing have made it possible to identify new targets rapidly and to repurpose approved drugs for treating heterogeneous diseases by the 'precise' targeting of individualized disease modules. In this study, we develop a Genome-wide Positioning Systems network (GPSnet) algorithm for drug repurposing by specifically targeting disease modules derived from individual patient's DNA and RNA sequencing profiles mapped to the human protein-protein interactome network. We investigate whole-exome sequencing and transcriptome profiles from ~5,000 patients across 15 cancer types from The Cancer Genome Atlas. We show that GPSnet-predicted disease modules can predict drug responses and prioritize new indications for 140 approved drugs. Importantly, we experimentally validate that an approved cardiac arrhythmia and heart failure drug, ouabain, shows potential antitumor activities in lung adenocarcinoma by uniquely targeting a HIF1α/LEO1-mediated cell metabolism pathway. In summary, GPSnet offers a network-based, in silico drug repurposing framework for more efficacious therapeutic selections.


Assuntos
Algoritmos , Reposicionamento de Medicamentos/métodos , Biologia de Sistemas/métodos , Adenocarcinoma de Pulmão/tratamento farmacológico , Adenocarcinoma de Pulmão/genética , Arritmias Cardíacas/tratamento farmacológico , Arritmias Cardíacas/genética , Simulação por Computador , Conjuntos de Dados como Assunto , Estudos de Viabilidade , Redes Reguladoras de Genes/efeitos dos fármacos , Insuficiência Cardíaca/tratamento farmacológico , Insuficiência Cardíaca/genética , Saúde Holística , Humanos , Subunidade alfa do Fator 1 Induzível por Hipóxia/metabolismo , Neoplasias Pulmonares/tratamento farmacológico , Neoplasias Pulmonares/genética , Redes e Vias Metabólicas/efeitos dos fármacos , Redes e Vias Metabólicas/genética , Terapia de Alvo Molecular/métodos , Ouabaína/farmacologia , Ouabaína/uso terapêutico , Mapas de Interação de Proteínas/efeitos dos fármacos , Mapas de Interação de Proteínas/genética , Fatores de Transcrição/metabolismo , Transcriptoma
11.
Nat Commun ; 10(1): 3015, 2019 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-31289271

RESUMO

The protein-protein interaction (PPI) network of an organism serves as a skeleton for its signaling circuitry, which mediates cellular response to environmental and genetic cues. Understanding this circuitry could improve the prediction of gene function and cellular behavior in response to diverse signals. To realize this potential, one has to comprehensively map PPIs and their directions of signal flow. While the quality and the volume of identified human PPIs improved dramatically over the last decade, the directions of these interactions are still mostly unknown, thus precluding subsequent prediction and modeling efforts. Here we present a systematic approach to orient the human PPI network using drug response and cancer genomic data. We provide a diffusion-based method for the orientation task that significantly outperforms existing methods. The oriented network leads to improved prioritization of cancer driver genes and drug targets compared to the state-of-the-art unoriented network.


Assuntos
Biologia Computacional/métodos , Neoplasias/genética , Mapeamento de Interação de Proteínas/métodos , Mapas de Interação de Proteínas/efeitos dos fármacos , Análise de Dados , Bases de Dados Genéticas/estatística & dados numéricos , Bases de Dados de Produtos Farmacêuticos/estatística & dados numéricos , Conjuntos de Dados como Assunto , Humanos , Mapas de Interação de Proteínas/genética , Software
12.
J Neuroinflammation ; 16(1): 136, 2019 Jul 04.
Artigo em Inglês | MEDLINE | ID: mdl-31272469

RESUMO

BACKGROUND: Current evidence indicates that extracellular vesicles (EVs) participate in intercellular signaling, and in the regulation and amplification of neuroinflammation. We have previously shown that ethanol activates glial cells through Toll-like receptor 4 (TLR4) by triggering neuroinflammation. Here, we evaluate if ethanol and the TLR4 response change the release and inflammatory content of astrocyte-derived EVs, and whether these vesicles are capable of communicating with neurons by spreading neuroinflammation. METHODS: Cortical neurons and astrocytes in culture were used. EVs were isolated from the extracellular medium of the primary culture of the WT and TLR4-KO astrocytes treated with or without ethanol (40 mM) for 24 h. Flow cytometry, nanoparticle tracking analysis technology, combined with exosomal molecular markers (tetraspanins) along with electron microscopy, were used to characterize and quantify EVs. The content of EVs in inflammatory proteins, mRNA, and miRNAs was analyzed by Western blot and RT-PCR in both astrocyte-derived EVs and the neurons incubated or not with these EVs. Functional analyses of miRNAs were also performed. RESULTS: We show that ethanol increases the number of secreted nanovesicles and their content by raising the levels of both inflammatory-related proteins (TLR4, NFκB-p65, IL-1R, caspase-1, NLRP3) and by changing miRNAs (mir-146a, mir-182, and mir-200b) in the EVs from the WT-astrocytes compared with those from the untreated WT cells. No changes were observed in either the number of isolated EVs or their content between the untreated and ethanol-treated TLR4-KO astrocytes. We also show that astrocyte-derived EVs could be internalized by naïve cortical neurons to increase the neuronal levels of inflammatory protein (COX-2) and miRNAs (e.g., mir-146a) and to compromise their survival. The functional analysis of miRNAs revealed the regulatory role of the expressed miRNAs in some genes involved in several inflammatory pathways. CONCLUSIONS: These results suggest that astrocyte-derived EVs could act as cellular transmitters of inflammation signaling by spreading and amplifying the neuroinflammatory response induced by ethanol through TLR4 activation.


Assuntos
Astrócitos/efeitos dos fármacos , Astrócitos/metabolismo , Etanol/toxicidade , Vesículas Extracelulares/efeitos dos fármacos , Vesículas Extracelulares/metabolismo , Receptor 4 Toll-Like/metabolismo , Animais , Células Cultivadas , Inflamação/induzido quimicamente , Inflamação/metabolismo , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Mapas de Interação de Proteínas/efeitos dos fármacos , Mapas de Interação de Proteínas/fisiologia , Receptor 4 Toll-Like/agonistas
13.
Artigo em Inglês | MEDLINE | ID: mdl-31281799

RESUMO

Nosocomial infections have become alarming with the increase of multidrug-resistant bacterial strains of Acinetobacter baumannii. Being the causative agent in ~80% of the cases, these pathogenic gram-negative species could be deadly for hospitalized patients, especially in intensive care units utilizing ventilators, urinary catheters, and nasogastric tubes. Primarily infecting an immuno-compromised system, they are resistant to most antibiotics and are the root cause of various types of opportunistic infections including but not limited to septicemia, endocarditis, meningitis, pneumonia, skin, and wound sepsis and even urinary tract infections. Conventional experimental methods including typing, computational methods encompassing comparative genomics, and combined methods of reverse vaccinology and proteomics had been proposed to differentiate and develop vaccines and/or drugs for several outbreak strains. However, identifying proteins suitable enough to be posed as drug targets and/or molecular vaccines against the multidrug-resistant pathogenic bacterial strains has probably remained an open issue to address. In these cases of novel protein identification, the targets either are uncharacterized or have been unable to confer the most coveted protection either in the form of molecular vaccine candidates or as drug targets. Here, we report a strategic approach with the 3,766 proteins from the whole genome of A. baumannii ATCC19606 (AB) to rationally identify plausible candidates and propose them as future molecular vaccine candidates and/or drug targets. Essentially, we started with mapping the vaccine candidates (VaC) and virulence factors (ViF) of A. baumannii strain AYE onto strain ATCC19606 to identify them in the latter. We move on to build small networks of VaC and ViF to conceptualize their position in the network space of the whole genomic protein interactome (GPIN) and rationalize their candidature for drugs and/or molecular vaccines. To this end, we propose new sets of known proteins unearthed from interactome built using key factors, KeF, potent enough to compete with VaC and ViF. Our method is the first of its kind to propose, albeit theoretically, a rational approach to identify crucial proteins and pose them for candidates of vaccines and/or drugs effective enough to combat the deadly pathogenic threats of A. baumannii.


Assuntos
Acinetobacter baumannii/efeitos dos fármacos , Antibacterianos/farmacologia , Vacinas Bacterianas/uso terapêutico , Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos , Vacinas Sintéticas/farmacologia , Infecções por Acinetobacter/tratamento farmacológico , Infecções por Acinetobacter/imunologia , Infecções por Acinetobacter/microbiologia , Infecções por Acinetobacter/prevenção & controle , Acinetobacter baumannii/genética , Proteínas de Bactérias/genética , Biologia Computacional , Infecção Hospitalar , Genoma Bacteriano , Genômica , Humanos , Mapas de Interação de Proteínas/efeitos dos fármacos , Mapas de Interação de Proteínas/genética , Proteômica , Fatores de Virulência/genética
14.
Biosci Biotechnol Biochem ; 83(11): 2034-2048, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31282289

RESUMO

Protein-protein interactions (PPIs) lead the formation of protein complexes that perform biochemical reactions that maintain the living state of the living cell. Although therapeutic drugs should influence the formation of protein complexes in addition to PPI network, the methodology analyzing such influences remain to be developed. Here, we demonstrate that a new approach combining HPLC (high performance liquid chromatography) for separating protein complexes, and the SILAC (stable isotope labeling using amino acids in cell culture) method for relative protein quantification, enable us to identify the protein complexes influenced by a drug. We applied this approach to the analysis of thalidomide action on HepG2 cells, assessed the identified proteins by clustering data analyses, and assigned 135 novel protein complexes affected by the drug. We propose that this approach is applicable to elucidating the mechanisms of actions of other therapeutic drugs on the PPI network, and the formation of protein complexes.


Assuntos
Aminoácidos/química , Avaliação Pré-Clínica de Medicamentos/métodos , Mapas de Interação de Proteínas/efeitos dos fármacos , Proteínas/química , Proteínas/metabolismo , Proteômica , Células Hep G2 , Humanos , Marcação por Isótopo , Talidomida/farmacologia
15.
Cells ; 8(7)2019 06 29.
Artigo em Inglês | MEDLINE | ID: mdl-31261944

RESUMO

Influenza is a highly contagious virus that causes seasonal epidemics and unpredictable pandemics. Four influenza virus types have been identified to date: A, B, C, and D, where only A-C are known to infect humans. Influenza A (IAV) and B (IBV) viruses are responsible for seasonal influenza epidemics in humans and are responsible for up to a billion flu infections annually. The M2 protein is present in all influenza types and belongs to the class of viroporins (i.e., small proteins that form ion channels that increase membrane permeability in virus-infected cells). In influenza A and B, AM2 and BM2 are predominantly proton channels, although they also show some permeability to monovalent cations. In contrast, M2 proteins in influenza C (ICV) and D (IDV), CM2 and DM2, appear to be especially selective for chloride ions, with possibly some permeability to protons. These differences point to different biological roles for M2 in types A and B versus C and D, which is also reflected in their sequences. AM2 is by far the best characterized viroporin, and mechanistic details and rationale of its acid activation, proton selectivity, unidirectionality and relative low conductance are just beginning to be understood. The present review summarizes the biochemical and structural aspects of influenza viroporins and discusses the most relevant aspects of function, inhibition and interaction with the host.


Assuntos
Antivirais/farmacologia , Influenza Humana/virologia , Canais Iônicos/metabolismo , Orthomyxoviridae/patogenicidade , Proteínas da Matriz Viral/metabolismo , Antivirais/uso terapêutico , Cloretos/metabolismo , Interações Hospedeiro-Patógeno/efeitos dos fármacos , Humanos , Influenza Humana/tratamento farmacológico , Canais Iônicos/antagonistas & inibidores , Orthomyxoviridae/metabolismo , Mapas de Interação de Proteínas/efeitos dos fármacos , Prótons , Proteínas da Matriz Viral/antagonistas & inibidores
16.
Mol Med Rep ; 20(3): 2657-2666, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31322195

RESUMO

Glycyrrhizic acid (GA) is primarily used as an anti­inflammatory agent in cases of chronic hepatitis. However, its underlying mechanisms in diverse biological processes and its reported benefits are yet to be fully elucidated. In the current study, an analytical method based on pharmacogenomics was established to mine disease­modulatory activities mediated by GA. Five primary protein targets and 138 functional partners were identified for GA by querying open­source databases, including Drugbank and STRING. Subsequently, GA­associated primary and secondary protein targets were integrated into Cytoscape to construct a protein­protein interaction network to establish connectivity. GA­associated target genes were then clustered based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. The tumor necrosis factor axis was revealed to be a primary module regulated by GA­associated targets. Furthermore, 12 hub genes were queried to assess their potential anti­cancer effects using cBioPortal. The results indicated that pharmacogenomics­based analysis improved understanding of the underlying drug­target events of GA and provided predictive and definitive leads for future studies.


Assuntos
Anti-Inflamatórios/farmacologia , Redes Reguladoras de Genes/efeitos dos fármacos , Ácido Glicirrízico/farmacologia , Mapas de Interação de Proteínas/efeitos dos fármacos , Perfilação da Expressão Gênica , Ontologia Genética , Genômica/métodos , Humanos , Testes Farmacogenômicos , Fenótipo , Transdução de Sinais/efeitos dos fármacos
17.
Mol Med Rep ; 20(3): 2712-2724, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31322266

RESUMO

The purpose of the present study was to identify the potential targets and markers for diagnosis, therapy and prognosis in patients with prolactinoma at the molecular level and to determine the therapeutic effects of genipin in prolactinoma. The gene expression profiles of GSE2175, GSE26966 and GSE36314 were obtained from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) were identified after comparing between gene expression profiles of the prolactinoma tissues and normal tissues. Then, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and protein­protein interaction (PPI) network analysis were conducted. In addition, in vitro, scratch assay, colony­forming assay, Cell Counting Kit 8 (CCK8) assay and flow cytometry were performed to verify the functional effects of genipin. An aggregate of 12,695, 3,847 and 5,310 DEGs were identified from GSE2175, GSE26966 and GSE36314, respectively. The results of GO and KEGG analysis showed that the DEGs significant and important for prolactinoma were mostly involved with 'spindle pole' and 'oocyte meiosis'. A total of 20 genes were selected as hub genes with high degrees after PPI network analysis, including mitogen­activated protein kinase 1 (MAPK1), MYC, early growth response 1 (EGR1), Bcl2 and calmodulin 1 (CALM1). CCK8 assay, colony­forming assay and scratch assay were performed to verify the anti­prolactinoma effect of genipin. The results of flow cytometry showed that apoptosis was increased by genipin. MAPK1, MYC, EGR1, Bcl2 and CALM1 were screened as main hub genes. Genipin upregulated the expression level of EGR1 and p21 (downstream mediator of EGR1) and EGR1, inhibited the proliferation and migration of prolactinoma cells. Genipin is a promising drug for treatment of patients with prolactinoma.


Assuntos
Antineoplásicos/farmacologia , Iridoides/farmacologia , Neoplasias Hipofisárias/tratamento farmacológico , Neoplasias Hipofisárias/genética , Prolactinoma/tratamento farmacológico , Prolactinoma/genética , Animais , Apoptose/efeitos dos fármacos , Linhagem Celular Tumoral , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Redes Reguladoras de Genes/efeitos dos fármacos , Humanos , Camundongos , Mapas de Interação de Proteínas/efeitos dos fármacos , Ratos , Transcriptoma/efeitos dos fármacos
18.
Aquat Toxicol ; 214: 105235, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31271906

RESUMO

Corbicula fluminea is highly sensitive to ammonia, and its response mechanism to ammonia stress is unclear. In this study, C. fluminea was exposed to different levels of ammonia (control group, 10 mg/L, and 25 mg/L) for 24 h and 48 h. A comparative analysis of transcriptome sequencing (RNA-seq) of C. fluminea digestive gland showed that the expression of 6742 genes (11.54%) was significantly affected by ammonia stress. The TLR, NF-κB, FOXO, and apoptotic signaling pathways were involved in the regulation. The differential expression of 14 genes was confirmed by real-time PCR. In summary, the response mechanism of C. fluminea digestive gland under ammonia stress may be different from that of oxidative stress in marine vertebrates. Also, the NMDAR-mediated pathway may not be the main mechanism in the response to ammonia stress in C. fluminea. The present study is a preliminary study for further investigation into ammonia toxicity in shellfish.


Assuntos
Amônia/toxicidade , Corbicula/genética , Corbicula/fisiologia , Perfilação da Expressão Gênica , Estresse Fisiológico/genética , Animais , Corbicula/efeitos dos fármacos , Regulação da Expressão Gênica/efeitos dos fármacos , Ontologia Genética , Repetições de Microssatélites/genética , Anotação de Sequência Molecular , Polimorfismo de Nucleotídeo Único/genética , Mapas de Interação de Proteínas/efeitos dos fármacos , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Reprodutibilidade dos Testes , Estresse Fisiológico/efeitos dos fármacos , Transcriptoma/genética , Poluentes Químicos da Água/toxicidade
19.
Nat Commun ; 10(1): 3131, 2019 07 16.
Artigo em Inglês | MEDLINE | ID: mdl-31311925

RESUMO

Alterations in membrane proteins (MPs) and their regulated pathways have been established as cancer hallmarks and extensively targeted in clinical applications. However, the analysis of MP-interacting proteins and downstream pathways across human malignancies remains challenging. Here, we present a systematically integrated method to generate a resource of cancer membrane protein-regulated networks (CaMPNets), containing 63,746 high-confidence protein-protein interactions (PPIs) for 1962 MPs, using expression profiles from 5922 tumors with overall survival outcomes across 15 human cancers. Comprehensive analysis of CaMPNets links MP partner communities and regulated pathways to provide MP-based gene sets for identifying prognostic biomarkers and druggable targets. For example, we identify CHRNA9 with 12 PPIs (e.g., ERBB2) can be a therapeutic target and find its anti-metastasis agent, bupropion, for treatment in nicotine-induced breast cancer. This resource is a study to systematically integrate MP interactions, genomics, and clinical outcomes for helping illuminate cancer-wide atlas and prognostic landscapes in tumor homo/heterogeneity.


Assuntos
Biomarcadores Tumorais/genética , Redes Reguladoras de Genes , Neoplasias/genética , Receptores Nicotínicos/genética , Animais , Antineoplásicos/farmacologia , Antineoplásicos/uso terapêutico , Biomarcadores Tumorais/antagonistas & inibidores , Biomarcadores Tumorais/metabolismo , Bupropiona/farmacologia , Bupropiona/uso terapêutico , Linhagem Celular Tumoral , Conjuntos de Dados como Assunto , Feminino , Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Humanos , Estimativa de Kaplan-Meier , Camundongos , Neoplasias/tratamento farmacológico , Neoplasias/mortalidade , Antagonistas Nicotínicos/farmacologia , Antagonistas Nicotínicos/uso terapêutico , Prognóstico , Mapeamento de Interação de Proteínas/métodos , Mapas de Interação de Proteínas/efeitos dos fármacos , Mapas de Interação de Proteínas/genética , Receptores Nicotínicos/metabolismo , Ensaios Antitumorais Modelo de Xenoenxerto
20.
Int J Mol Sci ; 20(12)2019 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-31234416

RESUMO

Mutations in IQSEC2 cause intellectual disability (ID), which is often accompanied by seizures and autism. A number of studies have shown that IQSEC2 is an abundant protein in excitatory synapses and plays an important role in neuronal development as well as synaptic plasticity. Here, we review neuronal IQSEC2 signaling with emphasis on those aspects likely to be involved in autism. IQSEC2 is normally bound to N-methyl-D-aspartate (NMDA)-type glutamate receptors via post synaptic density protein 95 (PSD-95). Activation of NMDA receptors results in calcium ion influx and binding to calmodulin present on the IQSEC2 IQ domain. Calcium/calmodulin induces a conformational change in IQSEC2 leading to activation of the SEC7 catalytic domain. GTP is exchanged for GDP on ADP ribosylation factor 6 (ARF6). Activated ARF6 promotes downregulation of surface α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type glutamate receptors through a c-jun N terminal kinase (JNK)-mediated pathway. NMDA receptors, AMPA receptors, and PSD-95 are all known to be adversely affected in autism. An IQSEC2 transgenic mouse carrying a constitutively active mutation (A350V) shows autistic features and reduced levels of surface AMPA receptor subunit GluA2. Sec7 activity and AMPA receptor recycling are presented as two targets, which may respond to drug treatment in IQSEC2-associated ID and autism.


Assuntos
Transtorno Autístico/metabolismo , Fatores de Troca do Nucleotídeo Guanina/metabolismo , Deficiência Intelectual/metabolismo , Animais , Transtorno Autístico/tratamento farmacológico , Transtorno Autístico/genética , Fatores de Troca do Nucleotídeo Guanina/análise , Fatores de Troca do Nucleotídeo Guanina/genética , Humanos , Deficiência Intelectual/tratamento farmacológico , Deficiência Intelectual/genética , Terapia de Alvo Molecular , Mutação/efeitos dos fármacos , Mapas de Interação de Proteínas/efeitos dos fármacos , Transdução de Sinais/efeitos dos fármacos
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