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1.
Plant J ; 117(5): 1330-1343, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-37996996

RESUMO

Plants and bacteria have distinct pathways to synthesize the bioactive vitamin B1 thiamin diphosphate (TDP). In plants, thiamin monophosphate (TMP) synthesized in the TDP biosynthetic pathway is first converted to thiamin by a phosphatase, which is then pyrophosphorylated to TDP. In contrast, bacteria use a TMP kinase encoded by ThiL to phosphorylate TMP to TDP directly. The Arabidopsis THIAMIN REQUIRING2 (TH2)-encoded phosphatase is involved in TDP biosynthesis. The chlorotic th2 mutants have high TMP and low thiamin and TDP. Ectopic expression of Escherichia coli ThiL and ThiL-GFP rescued the th2-3 mutant, suggesting that the bacterial TMP kinase could directly convert TMP into TDP in Arabidopsis. These results provide direct evidence that the chlorotic phenotype of th2-3 is caused by TDP rather than thiamin deficiency. Transgenic Arabidopsis harboring engineered ThiL-GFP targeting to the cytosol, chloroplast, mitochondrion, or nucleus accumulated higher TDP than the wild type (WT). Ectopic expression of E. coli ThiL driven by the UBIQUITIN (UBI) promoter or an endosperm-specific GLUTELIN1 (GT1) promoter also enhanced TDP biosynthesis in rice. The pUBI:ThiL transgenic rice accumulated more TDP and total vitamin B1 in the leaves, and the pGT1:ThiL transgenic lines had higher TDP and total vitamin B1 in the seeds than the WT. Total vitamin B1 only increased by approximately 25-30% in the polished and unpolished seeds of the pGT1:ThiL transgenic rice compared to the WT. Nevertheless, these results suggest that genetic engineering of a bacterial vitamin B1 biosynthetic gene downstream of TMP can enhance vitamin B1 production in rice.


Assuntos
Arabidopsis , Arabidopsis/genética , Arabidopsis/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Ectópica do Gene , Tiamina/metabolismo , Tiamina Pirofosfato/genética , Tiamina Pirofosfato/metabolismo , Tiamina Monofosfato/metabolismo , Monoéster Fosfórico Hidrolases/metabolismo , Bactérias/metabolismo , Proteínas de Ligação a DNA/genética
2.
Sci Adv ; 9(5): eade0090, 2023 02 03.
Artigo em Inglês | MEDLINE | ID: mdl-36735780

RESUMO

Drosophila insulators were the first DNA elements found to regulate gene expression by delimiting chromatin contacts. We still do not know how many of them exist and what impact they have on the Drosophila genome folding. Contrary to vertebrates, there is no evidence that fly insulators block cohesin-mediated chromatin loop extrusion. Therefore, their mechanism of action remains uncertain. To bridge these gaps, we mapped chromatin contacts in Drosophila cells lacking the key insulator proteins CTCF and Cp190. With this approach, we found hundreds of insulator elements. Their study indicates that Drosophila insulators play a minor role in the overall genome folding but affect chromatin contacts locally at many loci. Our observations argue that Cp190 promotes cobinding of other insulator proteins and that the model, where Drosophila insulators block chromatin contacts by forming loops, needs revision. Our insulator catalog provides an important resource to study mechanisms of genome folding.


Assuntos
Proteínas de Drosophila , Drosophila , Animais , Drosophila/metabolismo , Cromatina/genética , Cromatina/metabolismo , Proteínas de Ligação a DNA/metabolismo , Proteínas de Drosophila/genética , Proteínas de Drosophila/metabolismo , Elementos Isolantes/genética , Proteínas Nucleares/metabolismo , Proteínas Associadas aos Microtúbulos/metabolismo , Fator de Ligação a CCCTC/genética , Fator de Ligação a CCCTC/metabolismo
3.
BMC Bioinformatics ; 22(Suppl 10): 634, 2022 Dec 08.
Artigo em Inglês | MEDLINE | ID: mdl-36482308

RESUMO

BACKGROUND: Recent increasing evidence indicates that three-dimensional chromosome structure plays an important role in genomic function. Topologically associating domains (TADs) are self-interacting regions that have been shown to be a chromosomal structural unit. During evolution, these are conserved based on checking synteny block cross species. Are there common TAD patterns across species or cell lines? RESULTS: To address the above question, we propose a novel task-TAD recognition-as opposed to traditional TAD identification. Specifically, we treat Hi-C maps as images, thus re-casting TAD recognition as image pattern recognition, for which we use a convolutional neural network and a residual neural network. In addition, we propose an elegant way to generate non-TAD data for binary classification. We demonstrate deep learning performance which is quite promising, AUC > 0.80, through cross-species and cell-type validation. CONCLUSIONS: TADs have been shown to be conserved during evolution. Interestingly, our results confirm that the TAD recognition model is practical across species, which indicates that TADs between human and mouse show common patterns from an image classification point of view. Our approach could be a new way to identify TAD variations or patterns among Hi-C maps. For example, TADs of two Hi-C maps are conserved if the two classification models are exchangeable.


Assuntos
Aprendizado Profundo , Humanos , Animais , Camundongos , Genômica
4.
ACS Omega ; 7(37): 33199-33215, 2022 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-36157723

RESUMO

The spontaneous combustion of underground minerals causes huge property losses and ecological damage. Coal and oil shale are co-associated minerals in the Fushun West Mine, and both have the ability to undergo oxidative spontaneous combustion. To study the effect of microstructure changes on the macroscopic gas product concentration during the mineral oxidation spontaneous combustion process in the Fushun West Mine, this study used a high-temperature temperature-programmed test to obtain the change trend of gas product concentration in different oxidation stages of minerals. Using Fourier transform infrared spectroscopy technology, the changes in active functional groups of surface molecules during the process of mineral oxidation and spontaneous combustion were identified. Finally, using the gray correlation degree, correlation analysis between the concentration of gas products and the concentration of active functional groups in different oxidation stages was carried out. The key reactive functional groups affecting mineral spontaneous combustion were identified. The essential reason for the change in the gas product was revealed.

5.
J Cell Mol Med ; 26(15): 4305-4321, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-35794816

RESUMO

Lung cancer is the leading cause of cancer-associated death, with a global 5-year survival rate <20%. Early metastasis and recurrence remain major challenges for lung cancer treatment. The stemness property of cancer cells has been suggested to play a key role in cancer plasticity, metastasis and drug-resistance, and is a potential target for drug development. In this study, we found that in non-small cell lung cancer (NSCLC), BMI1 and MCL1 play crucial roles of cancer stemness including invasion, chemo-resistance and tumour initiation. JNK signalling serves as a link between oncogenic pathway or genotoxicity to cancer stemness. The activation of JNK, either by mutant EGFR or chemotherapy agent, stabilized BMI1 and MCL1 proteins through suppressing the expression of E3-ubiquitin ligase HUWE1. In lung cancer patient samples, high level of BMI1 is correlated with poor survival, and the expression of BMI1 is positively correlated with MCL1. A novel small-molecule, BI-44, was developed, which effectively suppressed BMI1/MCL1 expressions and inhibited tumour formation and progression in preclinical models. Targeting cancer stemness mediated by BMI1/MCL1 with BI-44 provides the basis for a new therapeutic approach in NSCLC treatment.


Assuntos
Carcinoma Pulmonar de Células não Pequenas , Neoplasias Pulmonares , Carcinoma Pulmonar de Células não Pequenas/tratamento farmacológico , Carcinoma Pulmonar de Células não Pequenas/genética , Carcinoma Pulmonar de Células não Pequenas/metabolismo , Linhagem Celular Tumoral , Humanos , Neoplasias Pulmonares/tratamento farmacológico , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/metabolismo , Proteína de Sequência 1 de Leucemia de Células Mieloides/genética , Proteína de Sequência 1 de Leucemia de Células Mieloides/metabolismo , Células-Tronco Neoplásicas/metabolismo , Complexo Repressor Polycomb 1/genética , Complexo Repressor Polycomb 1/metabolismo , Proteínas Supressoras de Tumor/metabolismo , Ubiquitina-Proteína Ligases/genética , Ubiquitina-Proteína Ligases/metabolismo
6.
Toxicol In Vitro ; 81: 105346, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-35288263

RESUMO

PURPOSE: Pendulone, an isoflavone compound, is known to act against human cancer cells. However, its role in human non-small cell lung cancer (NSCLC) and the exact molecular mechanisms of action have never been reported. METHODS: We investigated the effects of pendulone on cell proliferation and apoptosis in human NSCLC H1299 cells. Cell viability was examined using the methyl-thiazol-diphenyl-tetrazolium (MTT) assay. Flow cytometry was employed to evaluate apoptotic indices such as the cell cycle, mitochondrial membrane potential, cytochrome c release, caspase activity, and death receptor expression. The expression of proteins related to the cell cycle and apoptosis were analyzed by Western blot analysis. RESULTS: Pendulone significantly decreased H1299 cell viability by inducing endoplasmic reticulum (ER) stress through the accumulation of reactive oxygen species (ROS). Pendulone induced the expression of ER stress-associated proteins, such as ATF4 and CHOP, which promoted the expression of death receptors. Activation of caspase 8 induced extrinsic pathway apoptosis. Pendulone also caused the loss of mitochondrial membrane potential, inhibited the anti-apoptotic proteins BCL-2 and activated the pro-apoptotic protein BAX, which promoted the release of cytochrome c to activate caspase 9. Antioxidant N-acetylcysteine (NAC), with its ROS-suppressive property, reversed pendulone-induced ER stress and cell apoptosis. CONCLUSION: Our findings provide evidence that pendulone induces apoptosis by inducing ER stress through ROS accumulation and mitochondrial dysfunction in NSCLC cell lines.


Assuntos
Carcinoma Pulmonar de Células não Pequenas , Isoflavonas , Neoplasias Pulmonares , Apoptose , Carcinoma Pulmonar de Células não Pequenas/tratamento farmacológico , Carcinoma Pulmonar de Células não Pequenas/metabolismo , Linhagem Celular Tumoral , Citocromos c/metabolismo , Estresse do Retículo Endoplasmático , Humanos , Isoflavonas/farmacologia , Neoplasias Pulmonares/metabolismo , Potencial da Membrana Mitocondrial , Quinonas , Espécies Reativas de Oxigênio/metabolismo
7.
BMC Bioinformatics ; 23(1): 64, 2022 Feb 10.
Artigo em Inglês | MEDLINE | ID: mdl-35144531

RESUMO

BACKGROUND: With the development of HiC technology, more and more HiC sequencing data have been produced. Although there are dozens of packages that can turn sequencing data into contact maps, there is no appropriate tool to query contact maps in order to extract biological information from HiC datasets. RESULTS: We present HiCmapTools, a tool for biologists to efficiently calculate and analyze HiC maps. The complete program provides multi-query modes and analysis tools. We have validated its utility on two real biological questions: TAD loop and TAD intra-density. CONCLUSIONS: HiCmapTools supports seven access options so that biologists can quantify contact frequency of the interest sites. The tool has been implemented in C++ and R and is freely available at https://github.com/changlabtw/hicmaptools and documented at https://hicmaptools.readthedocs.io/ .


Assuntos
Cromatina , Genômica
9.
IUBMB Life ; 74(2): 157-169, 2022 02.
Artigo em Inglês | MEDLINE | ID: mdl-34467634

RESUMO

Tumor-associated macrophages (TAMs) are a major component of the tumor microenvironment (TME) and are key cells in regulating tumor development, metastasis, immune responses, inflammation, and chemoresistance. In response to TME stimulation, circulating monocytes are recruited and differentiated as TAMs. Most TAMs are defined as alternatively activated (M2) phenotype to create immunosuppressive TME and support tumor progression. In contrast, classically activated (M1) TAMs can produce pro-inflammatory cytokines and enhance immune responses against tumor development. Autophagy is a conserved catabolic process to control cellular homeostasis and biological function. Emerging evidence reveals crucial contribution of autophagy in modulating TAM plasticity and functional polarization in TME. In this review, we introduce the current understanding of autophagy-regulated TAM function in development of cancer. We focus on how autophagy modulates antigen presentation, LC3-associated phagocytosis, cytokine secretion, inflammasome regulation, recruitment, differentiation, and polarization of TAMs and suggest strategies for potential therapeutics by targeting autophagy in TAMs. We expect this review can provide a new notion of future cancer immunotherapy.


Assuntos
Neoplasias , Macrófagos Associados a Tumor , Autofagia , Humanos , Imunoterapia , Neoplasias/metabolismo , Microambiente Tumoral
10.
Biomedicines ; 9(10)2021 Oct 10.
Artigo em Inglês | MEDLINE | ID: mdl-34680550

RESUMO

Failure to detect early-stage epithelial ovarian cancer (EOC) is a major contributing factor to its low survival rate. Increasing evidence suggests that different subtypes of EOC may behave as distinct diseases due to their different cells of origins, histology and treatment responses. Therefore, the identification of EOC subtype-specific biomarkers that can early detect the disease should be clinically beneficial. Exosomes are extracellular vesicles secreted by different types of cells and carry biological molecules, which play important roles in cell-cell communication and regulation of various biological processes. Multiple studies have proposed that exosomal miRNAs present in the circulation are good biomarkers for non-invasive early detection of cancer. In this review, the potential use of exosomal miRNAs as early detection biomarkers for EOCs and their accuracy are discussed. We also review the differential expression of circulating exosomal miRNAs and cell-free miRNAs between different biofluid sources, i.e., plasma and serum, and touch on the issue of endogenous reference miRNA selection. Additionally, the current clinical trials using miRNAs for detecting EOCs are summarized. In conclusion, circulating exosomal miRNAs as the non-invasive biomarkers have a high potential for early detection of EOC and its subtypes, and are likely to be clinically important in the future.

11.
Int J Mol Sci ; 22(18)2021 Sep 13.
Artigo em Inglês | MEDLINE | ID: mdl-34576028

RESUMO

Lung cancer is one of the most common cancers and the leading cause of death in humans worldwide. Non-small-cell lung cancer (NSCLC) accounts for approximately 85% of lung cancer cases and is often diagnosed at a late stage. Among patients with NSCLC, 50% die within 1 year after diagnosis. Even with clinical intervention, the 5-year survival rate is only approximately 20%. Therefore, the development of an advanced therapeutic strategy or novel agent is urgently required for treating NSCLC. Berberine exerts therapeutic activity toward NSCLC; therefore, its activity as an antitumor agent needs to be explored further. In this study, three terpenylated-bromide derivatives of berberrubine were synthesized and their anti-NSCLC activities were evaluated. Each derivative had higher anti-NSCLCs activity than berberrubine and berberine. Among them, 9-O-gernylberberrubine bromide (B4) and 9-O-farnesylberberrubine bromide (B5) showed greater growth inhibition, cell-cycle regulation, in vitro tumorigenesis suppression, and tumor migration reduction. In addition, some degree of apoptosis and autophagic flux blocking was noted in the cells under B4 and B5 treatments. Our study demonstrates that the berberrubine derivatives, B4 and B5, exhibit impressive anti-NSCLC activities and have potential for use as chemotherapeutic agents against NSCLC.


Assuntos
Berberina/análogos & derivados , Carcinoma Pulmonar de Células não Pequenas/tratamento farmacológico , Movimento Celular/efeitos dos fármacos , Proliferação de Células/efeitos dos fármacos , Células A549 , Antineoplásicos/farmacologia , Apoptose/efeitos dos fármacos , Berberina/síntese química , Berberina/química , Berberina/farmacologia , Brometos/química , Carcinogênese/efeitos dos fármacos , Carcinoma Pulmonar de Células não Pequenas/patologia , Humanos , Terpenos/síntese química , Terpenos/farmacologia
12.
Bioinformatics ; 37(11): 1506-1514, 2021 Jul 12.
Artigo em Inglês | MEDLINE | ID: mdl-30726875

RESUMO

MOTIVATION: Most evolutionary analyses are based on pre-estimated multiple sequence alignment. Wong et al. established the existence of an uncertainty induced by multiple sequence alignment when reconstructing phylogenies. They were able to show that in many cases different aligners produce different phylogenies, with no simple objective criterion sufficient to distinguish among these alternatives. RESULTS: We demonstrate that incorporating MSA induced uncertainty into bootstrap sampling can significantly increase correlation between clade correctness and its corresponding bootstrap value. Our procedure involves concatenating several alternative multiple sequence alignments of the same sequences, produced using different commonly used aligners. We then draw bootstrap replicates while favoring columns of the more unique aligner among the concatenated aligners. We named this concatenation and bootstrapping method, Weighted Partial Super Bootstrap (wpSBOOT). We show on three simulated datasets of 16, 32 and 64 tips that our method improves the predictive power of bootstrap values. We also used as a benchmark an empirical collection of 853 one to one orthologous genes from seven yeast species and found wpSBOOT to significantly improve discrimination capacity between topologically correct and incorrect trees. Bootstrap values of wpSBOOT are comparable to similar readouts estimated using a single method. However, for reduced trees by 50 and 95% bootstrap thresholds, wpSBOOT comes out the lowest Type I error (less FP). AVAILABILITY AND IMPLEMENTATION: The automated generation of replicates has been implemented in the T-Coffee package, which is available as open source freeware available from www.tcoffee.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

13.
Ann Thorac Surg ; 111(4): 1164-1173, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-32888924

RESUMO

BACKGROUND: A multiinstitutional study was conducted to analyze prognosticators of completely resected and pathologic T3 N0 M0 (pT3 N0 M0) stage thymic epithelial tumors. METHODS: A total of 607 patients with surgically treated thymic epithelial tumors between June 1988 and December 2017 were enrolled. A Cox proportional hazards model and an inverse probability of treatment weighting-adjusted analysis using the propensity score were performed. RESULTS: A total of 394 patients with thymoma and 130 patients with thymic carcinoma underwent complete tumor resections. Forty-one thymomas and 49 thymic carcinomas were confirmed as pT3 N0 M0 stage tumors. Postoperative adjuvant radiotherapy was associated with improved disease-free and overall survival in patients with thymoma (hazard ratio [HR], 0.40; 95% confidence interval [CI], 0.23 to 0.69; and HR, 0.24; 95% CI, 0.11 to 0.52, respectively) and in patients with thymic carcinoma (HR, 0.15; 95% CI, 0.07 to 0.33; and HR, 0.12; 95% CI, 0.05 to 0.31, respectively). Although lung invasion was associated with poor disease-free survival (HR, 3.28; 95% CI, 1.90 to 5.89) and overall survival (HR, 2.60; 95% CI, 1.21 to 6.07), male sex (HR, 1.88; 95% CI, 1.10 to 3.18), older age (HR, 2.77; 95% CI, 1.29 to 5.70), and advanced histologic features (HR, 3.84; 95% CI, 1.42 to 14.51) were associated with poor overall survival in patients with pT3 N0 M0 thymoma. Adjuvant chemotherapy was associated with improved disease-free survival (HR, 0.11; 95% CI, 0.03 to 0.41) and overall survival (HR, 0.11; 95% CI, 0.06 to 0.20) in patients with pT3 N0 M0 thymic carcinoma with superior vena cava or innominate vein invasion. CONCLUSIONS: Postoperative radiotherapy was associated with improved survival in patients with pT3 N0 M0 thymic epithelial tumors. Lung invasion was associated with poor survival in patients with pT3 N0 M0 thymoma. Adjuvant chemotherapy was associated with improved survival in patients with pT3 N0 M0 thymic carcinoma with superior vena cava or innominate vein invasion.


Assuntos
Estadiamento de Neoplasias/métodos , Neoplasias Epiteliais e Glandulares/diagnóstico , Timectomia , Neoplasias do Timo/diagnóstico , Intervalo Livre de Doença , Feminino , Seguimentos , Humanos , Masculino , Pessoa de Meia-Idade , Neoplasias Epiteliais e Glandulares/cirurgia , Prognóstico , Pontuação de Propensão , Estudos Retrospectivos , Neoplasias do Timo/cirurgia
14.
BMC Bioinformatics ; 21(Suppl 6): 276, 2020 Nov 18.
Artigo em Inglês | MEDLINE | ID: mdl-33203348

RESUMO

BACKGROUND: Biological data has grown explosively with the advance of next-generation sequencing. However, annotating protein function with wet lab experiments is time-consuming. Fortunately, computational function prediction can help wet labs formulate biological hypotheses and prioritize experiments. Gene Ontology (GO) is a framework for unifying the representation of protein function in a hierarchical tree composed of GO terms. RESULTS: We propose GODoc, a general protein GO prediction framework based on sequence information which combines feature engineering, feature reduction, and a novel ​k​-nearest-neighbor algorithm to resolve the multiple GO prediction problem. Comprehensive evaluation on CAFA2 shows that GODoc performs better than two baseline models. In the CAFA3 competition (68 teams), GODoc ranks 10th in Cellular Component Ontology. Regarding the species-specific task, the proposed method ranks 10th and 8th in the eukaryotic Cellular Component Ontology and the prokaryotic Molecular Function Ontology, respectively. In the term-centric task, GODoc performs third and is tied for first for the biofilm formation of Pseudomonas aeruginosa and the long-term memory of Drosophila melanogaster, respectively. CONCLUSIONS: We have developed a novel and effective strategy to incorporate a training procedure into the k-nearest neighbor algorithm (instance-based learning) which is capable of solving the Gene Ontology multiple-label prediction problem, which is especially notable given the thousands of Gene Ontology terms.


Assuntos
Algoritmos , Drosophila melanogaster , Ontologia Genética , Proteínas , Animais , Biologia Computacional , Drosophila melanogaster/genética , Política , Proteínas/genética
15.
Int J Mol Sci ; 21(12)2020 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-32545770

RESUMO

Lung cancer is the leading cause of death in the world, and the most common type of lung cancer is non-small-cell lung cancer (NSCLC), accounting for 85% of lung cancer. Patients with NSCLC, when detected, are mostly in a metastatic stage, and over half of patients diagnosed with NSCLC die within one year after diagnosis; the 5-year survival rate is 24%. However, in patients with metastatic NSCLC, the 5-year survival rate is 6%. Therefore, development of a new therapeutic agent or strategy is urgent for NSCLCs. Berberine has been illustrated to be a therapeutic agent of NSCLC. In the present study, we synthesized six derivatives of berberine, and the anti-NSCLC activity of these agents was examined. Some of them exert increasing proliferation inhibition comparing with berberine. Further studies demonstrated that two of the most effective agents, 9-O-decylberberrubine bromide (B6) and 9-O-dodecylberberrubine bromide (B7), performed cell cycle regulation, in-vitro tumorigenesis inhibition and autophagic flux blocking, but not induction of cellular apoptosis in NSCLC cells. Moreover, B6 and B7 were determined to be green fluorescent and could be penetrated and localized in cellular mitochondria. Herein, B6 and B7, the berberine derivatives we synthesized, revealed better anti-NSCLC activity with berberine and may be used as therapeutic candidates for the treatment of NSCLCs.


Assuntos
Antineoplásicos/síntese química , Berberina/análogos & derivados , Brometos/síntese química , Carcinoma Pulmonar de Células não Pequenas/metabolismo , Neoplasias Pulmonares/metabolismo , Células A549 , Antineoplásicos/química , Antineoplásicos/farmacologia , Brometos/química , Brometos/farmacologia , Carcinoma Pulmonar de Células não Pequenas/tratamento farmacológico , Ciclo Celular/efeitos dos fármacos , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Sobrevivência Celular/efeitos dos fármacos , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Humanos , Neoplasias Pulmonares/tratamento farmacológico , Mitocôndrias/efeitos dos fármacos , Mitocôndrias/metabolismo , Estrutura Molecular
16.
Eur J Med Chem ; 191: 112118, 2020 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-32113126

RESUMO

Highly expressed in cancer 1 (Hec1) plays an essential role in mitosis and is correlated with cancer formation, progression, and survival. Phosphorylation of Hec1 by Nek2 kinase is essential for its mitotic function, thus any disruption of Hec1/Nek2 protein-protein interaction has potential for cancer therapy. We have developed T-1101 tosylate (9j tosylate, 9j formerly known as TAI-95), optimized from 4-aryl-N-pyridinylcarbonyl-2-aminothiazole of scaffold 9 by introducing various C-4' substituents to enhance potency and water solubility, as a first-in-class oral clinical candidate for Hec1 inhibition with potential for cancer therapy. T-1101 has good oral absorption, along with potent in vitro antiproliferative activity (IC50: 14.8-21.5 nM). It can achieve high concentrations in Huh-7 and MDA-MB-231 tumor tissues, and showed promise in antitumor activity in mice bearing human tumor xenografts of liver cancer (Huh-7), as well as of breast cancer (BT474, MDA-MB-231, and MCF7) with oral administration. Oral co-administration of T-1101 halved the dose of sorafenib (25 mg/kg to 12.5 mg/kg) required to exhibit comparable in vivo activity towards Huh-7 xenografts. Cellular events resulting from Hec1/Nek2 inhibition with T-1101 treatment include Nek2 degradation, chromosomal misalignment, and apoptotic cell death. A combination of T-1101 with either of doxorubicin, paclitaxel, and topotecan in select cancer cells also resulted in synergistic effects. Inactivity of T-1101 on non-cancerous cells, a panel of kinases, and hERG demonstrates cancer specificity, target specificity, and cardiac safety, respectively. Subsequent salt screening showed that T-1101 tosylate has good oral AUC (62.5 µM·h), bioavailability (F = 77.4%), and thermal stability. T-1101 tosylate is currently in phase I clinical trials as an orally administered drug for cancer therapy.


Assuntos
Antineoplásicos/farmacologia , Proteínas do Citoesqueleto/antagonistas & inibidores , Descoberta de Drogas , Quinases Relacionadas a NIMA/antagonistas & inibidores , Inibidores de Proteínas Quinases/farmacologia , Animais , Antineoplásicos/síntese química , Antineoplásicos/química , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Proteínas do Citoesqueleto/metabolismo , Relação Dose-Resposta a Droga , Ensaios de Seleção de Medicamentos Antitumorais , Humanos , Células K562 , Neoplasias Hepáticas Experimentais/tratamento farmacológico , Neoplasias Hepáticas Experimentais/metabolismo , Neoplasias Hepáticas Experimentais/patologia , Camundongos , Camundongos SCID , Simulação de Acoplamento Molecular , Estrutura Molecular , Quinases Relacionadas a NIMA/metabolismo , Inibidores de Proteínas Quinases/síntese química , Inibidores de Proteínas Quinases/química , Relação Estrutura-Atividade , Distribuição Tecidual
17.
BMC Genomics ; 20(Suppl 9): 906, 2019 Dec 24.
Artigo em Inglês | MEDLINE | ID: mdl-31874640

RESUMO

BACKGROUND: Tandem mass spectrometry allows biologists to identify and quantify protein samples in the form of digested peptide sequences. When performing peptide identification, spectral library search is more sensitive than traditional database search but is limited to peptides that have been previously identified. An accurate tandem mass spectrum prediction tool is thus crucial in expanding the peptide space and increasing the coverage of spectral library search. RESULTS: We propose MS2CNN, a non-linear regression model based on deep convolutional neural networks, a deep learning algorithm. The features for our model are amino acid composition, predicted secondary structure, and physical-chemical features such as isoelectric point, aromaticity, helicity, hydrophobicity, and basicity. MS2CNN was trained with five-fold cross validation on a three-way data split on the large-scale human HCD MS2 dataset of Orbitrap LC-MS/MS downloaded from the National Institute of Standards and Technology. It was then evaluated on a publicly available independent test dataset of human HeLa cell lysate from LC-MS experiments. On average, our model shows better cosine similarity and Pearson correlation coefficient (0.690 and 0.632) than MS2PIP (0.647 and 0.601) and is comparable with pDeep (0.692 and 0.642). Notably, for the more complex MS2 spectra of 3+ peptides, MS2PIP is significantly better than both MS2PIP and pDeep. CONCLUSIONS: We showed that MS2CNN outperforms MS2PIP for 2+ and 3+ peptides and pDeep for 3+ peptides. This implies that MS2CNN, the proposed convolutional neural network model, generates highly accurate MS2 spectra for LC-MS/MS experiments using Orbitrap machines, which can be of great help in protein and peptide identifications. The results suggest that incorporating more data for deep learning model may improve performance.


Assuntos
Redes Neurais de Computação , Espectrometria de Massas em Tandem/métodos , Aprendizado Profundo , Células HeLa , Humanos , Peptídeos/química , Proteínas/química , Análise de Sequência de Proteína
18.
Int J Mol Sci ; 20(22)2019 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-31766223

RESUMO

ß-catenin is a major component of the Wnt/ß-catenin signaling pathway, and is known to play a role in lung tumorigenesis. ß-catenin-interacting protein 1 (CTNNBIP1) is a known repressor of ß-catenin transactivation. However, little is known about the role of CTNNBIP1 in lung cancer. The aim of this study was to carry out a molecular analysis of CTNNBIP1 and its effect on ß-catenin signaling, using samples from lung cancer patients and various lung cancer cell lines. Our results indicate a significant inverse correlation between the CTNNBIP1 mRNA expression levels and the CTNNBIP1 promoter hypermethylation, which suggests that the promoter hypermethylation is responsible for the low levels of CTNNBIP1 present in many lung cancer patient samples. The ectopic expression of CTNNBIP1 is able to reduce the ß-catenin transactivation; this then brings about a decrease in the expression of ß-catenin-targeted genes, such as matrix metalloproteinase 7 (MMP7). Conversely, CTNNBIP1 knockdown is able to increase ß-catenin transactivation and the expression of MMP7. In agreement with these findings, a low level of CTNNBIP1 was found to be correlated with a high level of MMP7 when a publicly available microarray dataset for lung cancer was analyzed. Also, in agreement with the above, the ectopic expression of CTNNBIP1 inhibits the migration of lung cancer cells, whereas the CTNNBIP1 knockdown increases cancer cell migration. Our findings suggest that CTNNBIP1 is a suppressor of cancer migration, thus making it a potential prognostic predictor for lung cancer.


Assuntos
Regulação Neoplásica da Expressão Gênica , Neoplasias Pulmonares/genética , beta Catenina/genética , Linhagem Celular Tumoral , Movimento Celular , Feminino , Humanos , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/patologia , Masculino , Via de Sinalização Wnt , beta Catenina/metabolismo
19.
BMC Endocr Disord ; 19(1): 16, 2019 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-30691427

RESUMO

BACKGROUND: Renal hyperparathyroidism is a common complication of chronic kidney disease (CKD) or end-stage renal disease (ESRD) characterized by elevated parathyroid hormone levels secondary to derangements in the homeostasis of calcium, phosphate, and vitamin D. Rapid correction of severe and prolonged hyperparathyroidism by surgical parathyroidectomy in long-term hemodialysis patients occasionally causes hungry bone syndrome. These patients then exhibit severe and long-lasting secondary or tertiary hyperparathyroidism with high bone turnover. CASE PRESENTATION: We report a case of recurrent tertiary hyperparathyroidism after total parathyroidectomy due to supernumerary parathyroid gland in a patient with long-term hemodialysis. Supplementation with intravenous calcium, oral calcium, and vitamin D immediately after patient surgery helps to prevent and treat hungry bone syndrome. CONCLUSIONS: We should prompt a search for the supernumerary parathyroid glands in ESRD patients, who have recurrent or persistent hyperparathyroidism after total parathyroidectomy. ESRD patients are more likely to develop hungry bone syndrome after parathyroidectomy. Prevention and treatment of hungry bone syndrome may be required after ectopic parathyroidectomy in clinical practice.


Assuntos
Hiperparatireoidismo/etiologia , Glândulas Paratireoides/patologia , Paratireoidectomia/efeitos adversos , Diálise Renal/efeitos adversos , Idoso , Humanos , Hiperparatireoidismo/cirurgia , Falência Renal Crônica/terapia , Masculino , Glândulas Paratireoides/cirurgia , Prognóstico , Recidiva
20.
Pharmacol Res ; 139: 41-49, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30391354

RESUMO

Irinotecan (CPT-11), a first-line chemotherapy for advanced colorectal cancer, causes serious diarrhea in patients receiving treatment. The underlying mechanism has been shown that the active metabolite of CPT-11, SN-38, is metabolized to the inactive metabolite SN-38 glucuronide (SN-38 G) during hepatic glucuronidation, and subsequently is exported into the intestine, where SN-38 G is hydrolyzed by bacterial ß-glucuronidase (ßG) to be SN-38, thus leading to intestinal toxicity. Thus, inhibition of the intestinal bacterial ßG activity is expected to prevent CPT-11-induced diarrhea. However, the effects of such inhibition on serum pharmacokinetics of SN-38, the key determinant of CPT-11 treatment, are uncertain. Here, we determined the effects of a potent E. coli ßG (eßG)-specific inhibitor pyrazolo[4,3-c]quinoline derivative (TCH-3562) for the potential use in preventing CPT-11-induced diarrhea. TCH-3562 exhibited efficacious inhibitory potency of endogenous ßG activity in two anaerobes, Eubacteriumsp. and Peptostreptococcus anaerobius. Oral administration of TCH-3562 also effectively reduced the bacterial ßG activity in mice intestine. Moreover, pharmacokinetic analysis of TCH-3562 revealed a relatively low amount of TCH-3562 was detected in the plasma whereas the majority of TCH-3562 was found in the feces. Importantly, co-treatment of CPT-11 and TCH-3562 did not decrease active SN-38 level in mice plasma. Finally, we established that TCH-3562 as an adjuvant treatment showed protective effects on CPT-11-induced diarrhea and had no negative effects on the therapeutic efficacy of CPT-11 in tumor-bearing mice. Therefore, inhibition of the intestinal bacterial ßG activity by the specific inhibitor, TCH-3562, is promising to prevent CPT-11-induced diarrhea while maintaining its anti-tumor efficacy that may have clinical potentials for the treatment with CPT-11.


Assuntos
Antineoplásicos Fitogênicos/uso terapêutico , Proteínas de Bactérias/antagonistas & inibidores , Neoplasias do Colo/tratamento farmacológico , Diarreia/prevenção & controle , Glucuronidase/antagonistas & inibidores , Irinotecano/uso terapêutico , Quinolinas/farmacologia , Animais , Linhagem Celular Tumoral , Diarreia/induzido quimicamente , Escherichia coli/efeitos dos fármacos , Escherichia coli/crescimento & desenvolvimento , Eubacterium/enzimologia , Células HEK293 , Humanos , Masculino , Camundongos Endogâmicos BALB C , Peptostreptococcus/enzimologia
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