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INTRODUCTION: Acute kidney injury (AKI) is a common clinical syndrome associated with high morbidity and mortality. Inhibition of the methyltransferase enhancer of zeste homolog 2 (EZH2) by its inhibitor 3-deazaneplanocin A (3-DZNeP) exerts renal benefits in acute renal ischemia-reperfusion injury (IRI). However, the underlying mechanisms are not completely known. This study aimed to elucidate the pathological mechanism of EZH2 in renal IRI by combination of multi-omics analysis and expression profiling in a public clinical cohort. METHODS: In this study, C57BL/6 J mice were used to establish the AKI model, which were treated with 3-DZNeP for 24 h. Kidney samples were collected for RNA-seq analysis, which was combined with publicly available EZH2 chromatin immunoprecipitation sequencing (ChIP-seq) data of mouse embryonic stem cell for a joint analysis to identify differentially expressed genes. Several selected differentially expressed genes were verified by quantitative PCR. Finally, single-nucleus sequencing data and expression profiling in public clinical datasets were used to confirm the negative correlation of the selected genes with EZH2 expression. RESULTS: 3-DZNeP treatment significantly improved renal pathology and function in IRI mice. Through RNA-seq analysis combined with EZH2 ChIP-seq database, 162 differentially expressed genes were found, which might be involved in EZH2-mediated pathology in IRI kidneys. Four differential expressed genes (Scd1, Cidea, Ghr, and Kl) related to lipid metabolism or cell growth were selected based on Gene Ontology and Kyoto Encyclopedia of Genes and Genome enrichment analysis, which were validated by quantitative PCR. Data from single-nucleus RNA sequencing revealed the negative correlation of these four genes with Ezh2 expression in different subpopulations of proximal tubular cells in IRI mice in a different pattern. Finally, the negative correlation of these four genes with EZH2 expression was confirmed in patients with AKI in two clinical datasets. CONCLUSIONS: Our study indicates that Scd1, Cidea, Ghr, and Kl are downstream genes regulated by EZH2 in AKI. Upregulation of EZH2 in AKI inhibits the expression of these four genes in a different population of proximal tubular cells to minimize normal physiological function and promote acute or chronic cell injuries following AKI.
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Lesión Renal Aguda , Adenosina , Adenosina/análogos & derivados , Proteína Potenciadora del Homólogo Zeste 2 , Ratones Endogámicos C57BL , Daño por Reperfusión , Animales , Proteína Potenciadora del Homólogo Zeste 2/antagonistas & inhibidores , Proteína Potenciadora del Homólogo Zeste 2/metabolismo , Daño por Reperfusión/tratamiento farmacológico , Ratones , Adenosina/farmacología , Lesión Renal Aguda/tratamiento farmacológico , Lesión Renal Aguda/prevención & control , Lesión Renal Aguda/metabolismo , Lesión Renal Aguda/etiología , Masculino , Riñón/efectos de los fármacos , Riñón/patología , Riñón/metabolismo , MultiómicaRESUMEN
Per- and polyfluoroalkyl substances (PFASs) have potential to accumulate in crops and pose health risks to humans, but it is unclear how the widely present organic matters in soil, such as humic acid (HA), affect their uptake and translocation in plants. In this study, hydroponic experiments were conducted to systematically disclose the impacts of HA on the uptake, translocation, and transmembrane transport at the subcellular level of four PFASs, including perfluorooctane sulfonic acid, perfluorooctanoic acid, perfluorohexane sulfonic acid, and 6:2 chlorinated polyfluoroalkyl ether sulfonate in wheat (Triticum aestivum L.). The results of the uptake and depuration experiments indicated that HA depressed the adsorption and absorption of PFASs in wheat roots by reducing the bioavailability of PFASs, and HA did not affect the long-range transport of PFASs to be eliminated via the phloem of wheat. However, HA facilitated their transmembrane transport in wheat roots, while the contrary effect was observed in the shoots. The inhibitor experiments coupled with transcriptomics analysis uncover that the increased transmembrane transport of PFASs stimulated by HA is mainly driven by the slow-type anion channel pathways interacting with Ca2+-dependent protein kinases (Ca2+-CDPK-SLAC1). The promoted transmembrane transport of PFASs might cause adverse effects on the plant cell wall, which causes further concerns.
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Ácidos Alcanesulfónicos , Fluorocarburos , Humanos , Sustancias Húmicas/análisis , Triticum , Ácidos Alcanesulfónicos/análisis , Ácidos Alcanesulfónicos/metabolismo , Suelo , Alcanosulfonatos/análisis , Fluorocarburos/análisis , ChinaRESUMEN
The Bromodomain and Extra-terminal domain (BET) proteins are promising targets in treating cancers. Although BET inhibitors have been in clinical trials, they are limited by lacking of suitable biomarkers to indicate drug responses in different cancers. Here we identify DHRS2, ETV4 and NOTUM as potential biomarkers to indicate drug resistance in liver cancer cells of a recently discovered BET inhibitor, Hjp-6-171. Furthermore, we confirm that reactivation of WNT pathway, the target of NOTUM, contributes to the drug sensitivity restoration in Hjp-6-171 resistant cells. Specially, combinations of Hjp-6-171 and a GSK3ß inhibitor CHIR-98014 show remarkable therapeutic effects in vitro and in vivo. Integrating RNA-seq and ChIP-seq data, we reveal the expression signature of ß-catenin regulated genes is contrary in sensitive cells to that in resistant cells. We propose WNT signaling molecules such as ß-catenin and ETV4 to be candidate biomarkers to indicate BET inhibitor responses in liver cancer patients.
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Neoplasias Hepáticas , Vía de Señalización Wnt , Carbonil Reductasa (NADPH)/genética , Carbonil Reductasa (NADPH)/metabolismo , Línea Celular Tumoral , Proliferación Celular/genética , Regulación Neoplásica de la Expresión Génica , Humanos , Neoplasias Hepáticas/tratamiento farmacológico , Neoplasias Hepáticas/genética , Vía de Señalización Wnt/genética , beta Catenina/genética , beta Catenina/metabolismoRESUMEN
Circular RNAs (circRNAs) are emerging species of mRNA splicing products with largely unknown functions. Although several computational pipelines for circRNA identification have been developed, these methods strictly rely on uniquely mapped reads overlapping back-splice junctions (BSJs) and lack approaches to model the statistical significance of the identified circRNAs. Here, we reported a systematic computational approach to identify circRNAs by simultaneously utilizing BSJ overlapping reads and discordant BSJ spanning reads to identify circRNAs. Moreover, we developed a novel procedure to estimate the P-values of the identified circRNAs. A computational cross-validation and experimental validations demonstrated that our method performed favorably compared to existing circRNA detection tools. We created a standalone tool, CircRNAFisher, to implement the method, which might be valuable to computational and experimental scientists studying circRNAs.
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Biología Computacional/métodos , ARN/análisis , Análisis de Secuencia de ARN/métodos , Algoritmos , Línea Celular Tumoral , Fibroblastos/química , Humanos , ARN/genética , ARN/aislamiento & purificación , ARN CircularRESUMEN
Epithelial-to-mesenchymal transition (EMT) is a complex multistep process in which phenotype switches are mediated by a network of transcription factors (TFs). Systematic characterization of all dynamic TFs controlling EMT state transitions, especially for the intermediate partial-EMT state, represents a highly relevant yet largely unexplored task. Here, we performed a computational analysis that integrated time-course EMT transcriptomic data with public cistromic data and identified three synergistic master TFs (ETS2, HNF4A and JUNB) that regulate the transition through the partial-EMT state. Overexpression of these regulators predicted a poor clinical outcome, and their elimination readily abolished TGF-ß-induced EMT. Importantly, these factors utilized a clique motif, physically interact and their cumulative binding generally characterized EMT-associated genes. Furthermore, analyses of H3K27ac ChIP-seq data revealed that ETS2, HNF4A and JUNB are associated with super-enhancers and the administration of BRD4 inhibitor readily abolished TGF-ß-induced EMT. These findings have implications for systematic discovery of master EMT regulators and super-enhancers as novel targets for controlling metastasis.
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Adenocarcinoma/genética , Transición Epitelial-Mesenquimal/genética , Regulación Neoplásica de la Expresión Génica , Factor Nuclear 4 del Hepatocito/genética , Neoplasias Pulmonares/genética , Proteína Proto-Oncogénica c-ets-2/genética , Factores de Transcripción/genética , Adenocarcinoma/metabolismo , Adenocarcinoma/mortalidad , Adenocarcinoma/patología , Adenocarcinoma del Pulmón , Antineoplásicos/farmacología , Azepinas/farmacología , Proteínas de Ciclo Celular , Línea Celular Tumoral , Células Epiteliales/efectos de los fármacos , Células Epiteliales/metabolismo , Células Epiteliales/patología , Transición Epitelial-Mesenquimal/efectos de los fármacos , Perfilación de la Expresión Génica , Factor Nuclear 4 del Hepatocito/antagonistas & inhibidores , Factor Nuclear 4 del Hepatocito/metabolismo , Histonas/genética , Histonas/metabolismo , Humanos , Neoplasias Pulmonares/metabolismo , Neoplasias Pulmonares/mortalidad , Neoplasias Pulmonares/patología , Proteínas Nucleares/antagonistas & inhibidores , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Fenotipo , Proteína Proto-Oncogénica c-ets-2/antagonistas & inhibidores , Proteína Proto-Oncogénica c-ets-2/metabolismo , ARN Interferente Pequeño/genética , ARN Interferente Pequeño/metabolismo , Análisis de Secuencia de ARN , Transducción de Señal , Proteína smad3/genética , Proteína smad3/metabolismo , Análisis de Supervivencia , Factores de Transcripción/antagonistas & inhibidores , Factores de Transcripción/metabolismo , Transcriptoma , Factor de Crecimiento Transformador beta/farmacología , Triazoles/farmacologíaRESUMEN
BACKGROUND: T674I FIP1L1-PDGFRα in a subset of chronic eosinophilic leukemia (CEL) is a gatekeeper mutation that is resistant to many tyrosine kinase inhibitors (TKIs) (e.g., imatinib, nilotinib and dasatinib), similar to T315I Bcr-Abl. Therefore, novel TKIs effective against T674I FIP1L1-PDGFRα are needed. Ponatinib (AP24534) is a novel orally bioavailable TKI against T315I Bcr-Abl, but it is not clear whether ponatinib is effective against T674I FIP1L1-PDGFRα. The purpose of this study was to examine the effect of ponatinib on T674I FIP1L1-PDGFRα. METHODS: Molecular docking analysis in silico was performed. The effects of ponatinib on PDGFRα signaling pathways, apoptosis and cell cycling were examined in EOL-1, BaF3 cells expressing either wild type (WT) or T674I FIP1L1-PDGFRα. The in vivo antitumor activity of ponatinib was evaluated with xenografted BaF3-T674I FIP1L1-PDGFRα cells in nude mice models. RESULTS: Molecular docking analysis revealed that ponatinib could bind to the DFG (Asp-Phe-Gly)-out state of T674I PDGFRα. Ponatinib potently inhibited the phosphorylation of WT and T674I FIP1L1-PDGFRα and their downstream signaling molecules (e.g., Stat3, Stat5). Ponatinib strikingly inhibited the growth of both WT and T674I FIP1L1-PDGFRα-carrying CEL cells (IC50: 0.004-2.5 nM). It induced apoptosis in CEL cells with caspase-3-dependent cleavage of Mcl-1, and inhibited tyrosine phosphorylation of ß-catenin to decrease its stability and pro-survival functions. In vivo, ponatinib abrogated the growth of xenografted BaF3-T674I FIP1L1-PDGFRα cells in nude mice. CONCLUSIONS: Ponatinib is a pan-FIP1L1-PDGFRα inhibitor, and clinical trials are warranted to investigate its efficacy in imatinib-resistant CEL.
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Antineoplásicos/farmacología , Síndrome Hipereosinofílico/metabolismo , Imidazoles/farmacología , Piridazinas/farmacología , Animales , Apoptosis/efectos de los fármacos , Proliferación Celular/efectos de los fármacos , Resistencia a Antineoplásicos/efectos de los fármacos , Ensayo de Cambio de Movilidad Electroforética , Técnica del Anticuerpo Fluorescente , Humanos , Síndrome Hipereosinofílico/genética , Masculino , Ratones , Ratones Endogámicos BALB C , Ratones Desnudos , Microscopía Electrónica de Transmisión , Simulación del Acoplamiento Molecular , Proteína 1 de la Secuencia de Leucemia de Células Mieloides/metabolismo , Proteínas de Fusión Oncogénica/genética , Receptor alfa de Factor de Crecimiento Derivado de Plaquetas/genética , Transfección , Ensayos Antitumor por Modelo de Xenoinjerto , beta Catenina/metabolismo , Factores de Escisión y Poliadenilación de ARNm/genéticaRESUMEN
A series of novel indolin-2-ones inhibitors against p90 ribosomal S6 protein kinase 2 (RSK2) were designed and synthesized and their structure-activity relationship (SAR) was studied. The most potent inhibitor, compound 3s, exhibited potent inhibition against RSK2 with an IC50 value of 0.5 µM and presented a satisfactory selectivity against 23 kinases. The interactions of these inhibitors with RSK2 were investigated based on the proposed binding poses with molecular docking simulation. Four compounds and six compounds exhibited moderate anti-proliferation activities against PC 3 cells and MCF-7 cells, respectively.
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Indoles/química , Indoles/farmacología , Inhibidores de Proteínas Quinasas/química , Inhibidores de Proteínas Quinasas/farmacología , Proteínas Quinasas S6 Ribosómicas 90-kDa/antagonistas & inhibidores , Proteínas Quinasas S6 Ribosómicas 90-kDa/metabolismo , Antineoplásicos/química , Antineoplásicos/farmacología , Neoplasias de la Mama/tratamiento farmacológico , Línea Celular Tumoral , Proliferación Celular , Femenino , Humanos , Masculino , Simulación del Acoplamiento Molecular , Neoplasias de la Próstata/tratamiento farmacológico , Proteínas Quinasas S6 Ribosómicas 90-kDa/química , Relación Estructura-ActividadRESUMEN
The 90 kDa ribosomal S6 kinases (RSKs), especially RSK2, have attracted attention for the development of new anticancer agents. Through structural optimization of the hit compound 1 from our previous study, a series of barbituric acid aryl hydrazone analogues were designed and synthesized as potential RSK2 inhibitors. The most potent one, compound 9, showed a higher activity against RSK2 with an IC50 value of 1.95 µM. To analyze and elucidate their structure-activity relationship, the homology model of RSK2 N-terminal kinase domain was built and molecular docking simulations were performed, which provide helpful clues to design new inhibitors with desired activities.
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Barbitúricos/farmacología , Hidrazonas/farmacología , Inhibidores de Proteínas Quinasas/farmacología , Proteínas Quinasas S6 Ribosómicas 90-kDa/antagonistas & inhibidores , Barbitúricos/síntesis química , Barbitúricos/química , Relación Dosis-Respuesta a Droga , Humanos , Hidrazonas/síntesis química , Hidrazonas/química , Modelos Moleculares , Estructura Molecular , Inhibidores de Proteínas Quinasas/síntesis química , Inhibidores de Proteínas Quinasas/química , Proteínas Quinasas S6 Ribosómicas 90-kDa/metabolismo , Relación Estructura-ActividadRESUMEN
As alternatives of long-chain PFASs (Poly- and perfluoroalkyl substances), perfluoroalkyl phosphinic acids (PFPiAs) are increasingly observed in the environment, but their environmental behaviors have not been well understood. Here, the microbial biotransformation of C6/C6 and C8/C8 PFPiA in two soils (Soil N and Y) was investigated. After 252 d and 330 d of incubation with PFPiAs in Soil N and Y respectively, the levels of PFPiAs decreased distinctly, accompanied by the increasing perfluorohexaphosphonic acid (PFHxPA) or perfluorooctanophosphonic acid (PFOPA) formation, magnifying PFPiAs were susceptible to C-P cleavage, which was also confirmed by the density functional theory calculations. The half-lives of the PFPiAs were longer than one year, while generally shorter in Soil N than in Soil Y and that of C6/C6 was shorter than C8/C8 PFPiA (392 d and 746 d in Soil N, and 603 and 1155 d in Soil Y, respectively). Metagenomic sequencing analysis revealed that Proteobacteria as the primary host of the potential functional genes related to CP bond cleavage might be the crucial phyla contributing to the biotransformation of PFPiAs. Meanwhile, the more intensive interactions between the microbes in Soil N consistently contribute to its greater capacity for transforming PFPiAs.
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Fluorocarburos , Ácidos Fosfínicos , Ácidos Fosfínicos/metabolismo , Suelo , Semivida , Biotransformación , Fluorocarburos/análisisRESUMEN
Graphene oxide (GO) is a representative novel carbonaceous nanomaterial, and neonicotinoid insecticides (NEOs) are currently the insecticides with the highest market share in the world. Their widespread application deservedly leads to their release to the environment. Thus, the complex interactions of these two types of organic compounds have attracted extensive attention. In this study, the effects of GO and its derivatives, reduced GO (RGO) and oxidized GO (OGO), on the photolysis of imidacloprid (IMD) (a typical NEO) under ultraviolet (UV) irradiation were systematically investigated. The results showed that the presence of the graphene-based nanomaterials (GNs) largely depressed the photodegradation of IMD, and the inhibition degree followed the order of RGO > GO > OGO. This was because the sp2 π-conjugated structure in the GNs caused light-shielding effect and attenuated the direct photolysis of IMD, even though the GNs-generated reactive oxygen species (ROS) promoted the indirect photodegradation of IMD to a certain extent. Additionally, the rich O-functionalized GO and OGO altered the photolysis pathway of IMD and induced more toxic intermediate products. These results highlight the implication of carbonaceous nanomaterials on the behavior, fate and potential risk of NEOs in aqueous systems.
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Cancer cell membrane (CCM) derived nanotechnology functionalizes nanoparticles (NPs) to recognize homologous cells, exhibiting translational potential in accurate tumor therapy. However, these nanoplatforms are majorly generated from fixed cell lines and are typically evaluated in cell line-derived subcutaneous-xenografts (CDX), ignoring the tumor heterogeneity and differentiation from inter- and intra- individuals and microenvironments between heterotopic- and orthotopic-tumors, limiting the therapeutic efficiency of such nanoplatforms. Herein, various biomimetic nanoplatforms (CCM-modified gold@Carbon, i.e., Au@C-CCM) were fabricated by coating CCMs of head and neck squamous cell carcinoma (HNSCC) cell lines and patient-derived cells on the surface of Au@C NP. The generated Au@C-CCMs were evaluated on corresponding CDX, tongue orthotopic xenograft (TOX), immune-competent primary and distant tumor models, and patient-derived xenograft (PDX) models. The Au@C-CCM generates a photothermal conversion efficiency up to 44.2% for primary HNSCC therapy and induced immunotherapy to inhibit metastasis via photothermal therapy-induced immunogenic cell death. The homologous CCM endowed the nanoplatforms with optimal targeting properties for the highest therapeutic efficiency, far above those with mismatched CCMs, resulting in distinct tumor ablation and tumor growth inhibition in all four models. This work reinforces the feasibility of biomimetic NPs combining modular designed CMs and functional cores for customized treatment of HNSCC, can be further extended to other malignant tumors therapy.
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Neoplasias de Cabeza y Cuello , Terapia Fototérmica , Animales , Humanos , Carcinoma de Células Escamosas de Cabeza y Cuello/terapia , Xenoinjertos , Biomimética , Modelos Animales de Enfermedad , Neoplasias de Cabeza y Cuello/terapia , Línea Celular Tumoral , Microambiente TumoralRESUMEN
The introduction of the multi-objective optimization has dramatically changed the virtual combinatorial library design, which can consider many objectives simultaneously, such as synthesis cost and drug-likeness, thus may increase positive rates of biological active compounds. Here we described a software called CCLab (Combinatorial Chemistry Laboratory) for combinatorial library design based on the multi-objective genetic algorithm. Tests of the convergence ability and the ratio to re-take the building blocks in the reference library were conducted to assess the software in silico, and then it was applied to a real case of designing a 5×6 HDAC inhibitor library. Sixteen compounds in the resulted library were synthesized, and the histone deactetylase (HDAC) enzymatic assays proved that 14 compounds showed inhibitory ratios more than 50% against tested 3 HDAC enzymes at concentration of 20 µg/mL, with IC(50) values of 3 compounds comparable to SAHA. These results demonstrated that the CCLab software could enhance the hit rates of the designed library and would be beneficial for medicinal chemists to design focused library in drug development (the software can be downloaded at: http://202.127.30.184:8080/drugdesign.html).
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Algoritmos , Inhibidores de Histona Desacetilasas/química , Histona Desacetilasas/metabolismo , Diseño de Software , Técnicas Químicas Combinatorias , Inhibidores de Histona Desacetilasas/farmacología , Histona Desacetilasas/genética , Estructura Molecular , Relación Estructura-ActividadRESUMEN
Several potent and novel 11ß-hydroxysteroid dehydrogenase 1 (11ß-HSD1) inhibitors were discovered from in silico screening the commercially available Maybridge database. Among them, seven hit compounds showed good affinity, with IC(50) values lower than 100 nM and the best one 3.7 nM. To select the lead for further optimization, computational ADME/T prediction, the CYP3A4 inhibition and 11ß-HSD1 over 11ß-HSD2 selectivity test were also performed. Taking all of the above factors into consideration, two promising compounds were selected as lead structures for further development. The employed hierarchical virtual screening protocol not only demonstrates its efficiency, but also provides novel and selective compounds for developing 11ß-HSD1 inhibitors to protect against metabolic syndrome.
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11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/antagonistas & inhibidores , Diseño de Fármacos , Descubrimiento de Drogas/métodos , Inhibidores Enzimáticos/química , Inhibidores Enzimáticos/síntesis química , Síndrome Metabólico/prevención & control , 11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/genética , 11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 1/metabolismo , 11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 2/antagonistas & inhibidores , 11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 2/genética , 11-beta-Hidroxiesteroide Deshidrogenasa de Tipo 2/metabolismo , Animales , Simulación por Computador , Citocromo P-450 CYP3A/metabolismo , Inhibidores del Citocromo P-450 CYP3A , Bases de Datos Factuales , Evaluación Preclínica de Medicamentos , Inhibidores Enzimáticos/farmacocinética , Inhibidores Enzimáticos/farmacología , Células HEK293 , Ensayos Analíticos de Alto Rendimiento , Humanos , Concentración 50 Inhibidora , Síndrome Metabólico/tratamiento farmacológico , Síndrome Metabólico/patología , Ratones , Modelos Moleculares , Relación Estructura-ActividadRESUMEN
BACKGROUND: Genome sequencing and post-genomics projects such as structural genomics are extending the frontier of the study of sequence-structure-function relationship of genes and their products. Although many sequence/structure-based methods have been devised with the aim of deciphering this delicate relationship, there still remain large gaps in this fundamental problem, which continuously drives researchers to develop novel methods to extract relevant information from sequences and structures and to infer the functions of newly identified genes by genomics technology. RESULTS: Here we present an ultrafast method, named BSSF(Binding Site Similarity & Function), which enables researchers to conduct similarity searches in a comprehensive three-dimensional binding site database extracted from PDB structures. This method utilizes a fingerprint representation of the binding site and a validated statistical Z-score function scheme to judge the similarity between the query and database items, even if their similarities are only constrained in a sub-pocket. This fingerprint based similarity measurement was also validated on a known binding site dataset by comparing with geometric hashing, which is a standard 3D similarity method. The comparison clearly demonstrated the utility of this ultrafast method. After conducting the database searching, the hit list is further analyzed to provide basic statistical information about the occurrences of Gene Ontology terms and Enzyme Commission numbers, which may benefit researchers by helping them to design further experiments to study the query proteins. CONCLUSIONS: This ultrafast web-based system will not only help researchers interested in drug design and structural genomics to identify similar binding sites, but also assist them by providing further analysis of hit list from database searching.
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Biología Computacional/métodos , Proteínas/química , Programas Informáticos , Sitios de Unión , Estructura Secundaria de ProteínaRESUMEN
Protein kinases are attractive targets for therapeutic interventions in many diseases. Due to their importance in drug discovery, a kinase family-specific potential of mean force (PMF) scoring function, kinase-PMF, was developed to assess the binding of ATP-competitive kinase inhibitors. It is hypothesized that target-specific PMF scoring functions may achieve increased performance in scoring along with the growth of the PDB database. The kinase-PMF inherits the functions and atom types in PMF04 and uses a kinase data set of 872 complexes to derive the potentials. The performance of kinase-PMF was evaluated with an external test set containing 128 kinase crystal structures. We compared it with eight scoring functions commonly used in computer-aided drug design, either in terms of the retrieval rate of retrieving "right" conformations or a virtual screening study. The evaluation results clearly demonstrate that a target-specific scoring function is a promising way to improve prediction power in structure-based drug design compared with other general scoring functions. To provide this rescoring service for researchers, a publicly accessible Web site was established at http://202.127.30.184:8080/scoring/index.jsp .
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Diseño de Fármacos , Inhibidores de Proteínas Quinasas/química , Inhibidores de Proteínas Quinasas/farmacología , Proteínas Quinasas/metabolismo , Algoritmos , Ligandos , Conformación Molecular , Unión ProteicaRESUMEN
Background: Triple-negative breast cancer (TNBC) is an aggressive malignancy with high heterogeneity. However, the alternative polyadenylation (APA) profiles of TNBC remain unknown. Here, we aimed to define the characteristics of the APA events at post-transcription level among TNBCs. Methods: Using transcriptome microarray data, we analyzed APA profiles of 165 TNBC samples and 33 paired normal tissues. A pooled short hairpin RNA screen targeting 23 core cleavage and polyadenylation (C/P) genes was used to identify key C/P factors. Results: We established an unconventional APA subtyping system composed of four stable subtypes: 1) luminal androgen receptor (LAR), 2) mesenchymal-like immune-activated (MLIA), 3) basal-like (BL), 4) suppressed (S) subtypes. Patients in the S subtype had the worst disease-free survival comparing to other patients (log-rank p = 0.021). Enriched clinically actionable pathways and putative therapeutic APA events were analyzed among each APA subtype. Furthermore, CPSF1 and PABPN1 were identified as the master C/P factors in regulating APA events and TNBC proliferation. The depletion of CPSF1 or PABPN1 weakened cell proliferation, enhanced apoptosis, resulted in cell cycle redistribution and a reversion of APA events of genes associated with tumorigenesis, proliferation, metastasis and chemosensitivity in breast cancer. Conclusions: Our findings advance the understanding of tumor heterogeneity regulation in APA and yield new insights into therapeutic target identification in TNBC.
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Regulación Neoplásica de la Expresión Génica , Poliadenilación , Neoplasias de la Mama Triple Negativas/genética , Regiones no Traducidas 3'/genética , Apoptosis/genética , Mama/patología , Carcinogénesis/genética , Ciclo Celular/genética , Línea Celular Tumoral , Proliferación Celular/genética , Factor de Especificidad de Desdoblamiento y Poliadenilación/metabolismo , Supervivencia sin Enfermedad , Femenino , Heterogeneidad Genética , Humanos , Persona de Mediana Edad , Análisis de Secuencia por Matrices de Oligonucleótidos , Proteína I de Unión a Poli(A)/metabolismo , Estudios Prospectivos , RNA-Seq , Neoplasias de la Mama Triple Negativas/mortalidad , Neoplasias de la Mama Triple Negativas/patologíaRESUMEN
Rationale: Paclitaxel resistance is a major concern when treating triple-negative breast cancer (TNBC) patients. We aimed to identify candidates causing paclitaxel resistance and explore their significance in TNBC therapeutics. Methods: A genome-wide CRISPR screening, integrated with transcriptome analyses, was performed to identify candidates involved in paclitaxel-resistant TNBCs. Cell proliferation, cytotoxicity, immunofluorescent staining, and xenograft assays were conducted to verify the phenotypes of paclitaxel resistance induced by candidate genes, both in vitro and in vivo. RNA sequencing, Western blotting, and chromatin immunoprecipitation assays were used to explore the underlying mechanisms. Results: MEF2-interacting transcriptional repressor (MITR), the truncated isoform of histone deacetylase 9 (HDAC9) lacking the deacetylation domain, was enriched in paclitaxel-resistant cells. Elevated MITR expression resulted in increased interleukin-11 (IL11) expression and activation of downstream JAK/STAT3 signaling. Mechanistically, MITR counteracted MEF2A-induced transcriptional suppression of IL11, ultimately causing paclitaxel resistance. By contrast, pharmacological inhibition of JAK1/2 by ruxolitinib reversed paclitaxel resistance both in vitro and in vivo. Conclusion: Our in vitro and in vivo genetic and cellular analyses elucidated the pivotal role of MITR/MEF2A/IL11 axis in paclitaxel resistance and provided a novel therapeutic strategy for TNBC patients to overcome poor chemotherapy responses.
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Protocolos de Quimioterapia Combinada Antineoplásica/farmacología , Resistencia a Antineoplásicos/genética , Histona Desacetilasas/metabolismo , Paclitaxel/farmacología , Proteínas Represoras/metabolismo , Neoplasias de la Mama Triple Negativas/tratamiento farmacológico , Animales , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapéutico , Apoptosis/efectos de los fármacos , Apoptosis/genética , Línea Celular Tumoral , Proliferación Celular/efectos de los fármacos , Proliferación Celular/genética , Supervivencia Celular/efectos de los fármacos , Supervivencia Celular/genética , Conjuntos de Datos como Asunto , Resistencia a Antineoplásicos/efectos de los fármacos , Femenino , Regulación Neoplásica de la Expresión Génica/efectos de los fármacos , Regulación Neoplásica de la Expresión Génica/genética , Técnicas de Silenciamiento del Gen , Técnicas de Inactivación de Genes , Células HEK293 , Histona Desacetilasas/genética , Humanos , Interleucina-11/genética , Quinasas Janus/antagonistas & inhibidores , Quinasas Janus/metabolismo , Estimación de Kaplan-Meier , Factores de Transcripción MEF2/genética , Factores de Transcripción MEF2/metabolismo , Ratones , Nitrilos , Paclitaxel/uso terapéutico , Pirazoles/farmacología , Pirazoles/uso terapéutico , Pirimidinas , RNA-Seq , Proteínas Represoras/genética , Factor de Transcripción STAT3/metabolismo , Transducción de Señal/efectos de los fármacos , Transducción de Señal/genética , Neoplasias de la Mama Triple Negativas/genética , Neoplasias de la Mama Triple Negativas/mortalidad , Neoplasias de la Mama Triple Negativas/patología , Ensayos Antitumor por Modelo de XenoinjertoRESUMEN
The remarkable advances in next-generation sequencing technology have enabled the wide usage of sequencing as a clinical tool. To promote the advance of precision oncology for breast cancer in China, here we report a large-scale prospective clinical sequencing program using the Fudan-BC panel, and comprehensively analyze the clinical and genomic characteristics of Chinese breast cancer. The mutational landscape of 1,134 breast cancers reveals that the most significant differences between Chinese and Western patients occurred in the hormone receptor positive, human epidermal growth factor receptor 2 negative breast cancer subtype. Mutations in p53 and Hippo signaling pathways are more prevalent, and 2 mutually exclusive and 9 co-occurring patterns exist among 9 oncogenic pathways in our cohort. Further preclinical investigation partially suggests that NF2 loss-of-function mutations can be sensitive to a Hippo-targeted strategy. We establish a public database (Fudan Portal) and a precision medicine knowledge base for data exchange and interpretation. Collectively, our study presents a leading approach to Chinese precision oncology treatment and reveals potentially actionable mutations in breast cancer.
Asunto(s)
Pueblo Asiatico/genética , Neoplasias de la Mama , Terapia Molecular Dirigida , Mutación , Biomarcadores de Tumor/genética , Neoplasias de la Mama/genética , Neoplasias de la Mama/terapia , China , Manejo de Datos , Femenino , Marcadores Genéticos , Genómica , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Neurofibromina 2/genética , Oncogenes , Medicina de Precisión , Estudios Prospectivos , Transducción de Señal/genética , Proteína p53 Supresora de Tumor/genéticaRESUMEN
AIM: The search for molecules whose bioactivities are similar to those of given compounds or to optimize the initial lead compounds from high throughput screening has attracted increasing interest in recent years. Our goal is to provide a publically searchable database of scaffolds out from a large collection of existing chemical molecules. RESULTS: Although a number of in silico methods have emerged to facilitate this process, which has become known as "scaffold hopping" or "molecular hopping", there is an urgent need for a database system to provide such valuable data in the drug design field. Here we have systematically analyzed a collection of commercially available small molecule databases and a bioactive compound database to identify unique scaffolds and we have built a publically searchable database. The analysis of approximately 4,800,000 of these compounds identified 241,824 unique scaffolds, which are stored in a relational database (http://202.127.30.184:8080/db.html). Each entry in the database is associated with a molecular occurrence and includes its distribution of molecular properties, such as molecular weight, logP, hydrogen bond acceptor number, hydrogen bond donor number, rotatable bond number and ring number. More importantly, for scaffolds derived from the bioactive compounds database, it also contains the original compounds and their target information. CONCLUSION: This Web-based database system could help researchers in the fields of medicinal and organic chemistry to design novel molecules with properties similar to the original compounds, but built on novel scaffolds.