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1.
Cell ; 175(1): 186-199.e19, 2018 09 20.
Artículo en Inglés | MEDLINE | ID: mdl-30220457

RESUMEN

Mutations or aberrant upregulation of EZH2 occur frequently in human cancers, yet clinical benefits of EZH2 inhibitor (EZH2i) remain unsatisfactory and limited to certain hematological malignancies. We profile global posttranslational histone modification changes across a large panel of cancer cell lines with various sensitivities to EZH2i. We report here oncogenic transcriptional reprogramming mediated by MLL1's interaction with the p300/CBP complex, which directs H3K27me loss to reciprocal H3K27ac gain and restricts EZH2i response. Concurrent inhibition of H3K27me and H3K27ac results in transcriptional repression and MAPK pathway dependency in cancer subsets. In preclinical models encompassing a broad spectrum of EZH2-aberrant solid tumors, a combination of EZH2 and BRD4 inhibitors, or a triple-combination including MAPK inhibition display robust efficacy with very tolerable toxicity. Our results suggest an attractive precision treatment strategy for EZH2-aberrant tumors on the basis of tumor-intrinsic MLL1 expression and concurrent inhibition of epigenetic crosstalk and feedback MAPK activation.


Asunto(s)
Proteína Potenciadora del Homólogo Zeste 2/antagonistas & inhibidores , Proteína Potenciadora del Homólogo Zeste 2/genética , N-Metiltransferasa de Histona-Lisina/fisiología , Proteína de la Leucemia Mieloide-Linfoide/fisiología , Animales , Carcinogénesis/genética , Proteínas de Ciclo Celular , Línea Celular Tumoral , Epigénesis Genética/genética , Epigenómica/métodos , Femenino , Regulación Neoplásica de la Expresión Génica/genética , Código de Histonas/efectos de los fármacos , Código de Histonas/genética , N-Metiltransferasa de Histona-Lisina/genética , Histonas/genética , Histonas/fisiología , Humanos , Sistema de Señalización de MAP Quinasas , Masculino , Ratones , Ratones Endogámicos BALB C , Ratones SCID , Mutación , Proteína de la Leucemia Mieloide-Linfoide/genética , Proteínas Nucleares/metabolismo , Proteínas Nucleares/fisiología , Complejo Represivo Polycomb 2/metabolismo , Factores de Transcripción/metabolismo , Factores de Transcripción/fisiología , Activación Transcripcional , Ensayos Antitumor por Modelo de Xenoinjerto/métodos , Factores de Transcripción p300-CBP/fisiología
2.
Nature ; 2024 Jun 12.
Artículo en Inglés | MEDLINE | ID: mdl-38866052

RESUMEN

Increasing planting density is a key strategy to enhance maize yields1-3. An ideotype for dense planting requires a 'smart canopy' with leaf angles at different canopy layers differentially optimized to maximize light interception and photosynthesis4-6, amongst other features. Here, we identified leaf angle architecture of smart canopy 1 (lac1), a natural mutant possessing upright upper leaves, less erect middle leaves and relatively flat lower leaves. lac1 has improved photosynthetic capacity and weakened shade-avoidance responses under dense planting. lac1 encodes a brassinosteroid C-22 hydroxylase that predominantly regulates upper leaf angle. Phytochrome A photoreceptors accumulate in shade and interact with the transcription factor RAVL1 to promote its degradation via the 26S proteasome, thereby attenuating RAVL1 activation of lac1 and reducing brassinosteroid levels. This ultimately decreases upper leaf angle in dense fields. Large-scale field trials demonstrate lac1 boosts maize yields under high densities. To quickly introduce lac1 into breeding germplasm, we transformed a haploid inducer and recovered homozygous lac1 edits from 20 diverse inbred lines. The tested doubled haploids uniformly acquired smart-canopy-like plant architecture. We provide an important target and an accelerated strategy for developing high-density-tolerant cultivars, with lac1 serving as a genetic chassis for further engineering of a smart canopy in maize.

3.
Brief Bioinform ; 25(3)2024 Mar 27.
Artículo en Inglés | MEDLINE | ID: mdl-38770717

RESUMEN

Drug therapy is vital in cancer treatment. Accurate analysis of drug sensitivity for specific cancers can guide healthcare professionals in prescribing drugs, leading to improved patient survival and quality of life. However, there is a lack of web-based tools that offer comprehensive visualization and analysis of pancancer drug sensitivity. We gathered cancer drug sensitivity data from publicly available databases (GEO, TCGA and GDSC) and developed a web tool called Comprehensive Pancancer Analysis of Drug Sensitivity (CPADS) using Shiny. CPADS currently includes transcriptomic data from over 29 000 samples, encompassing 44 types of cancer, 288 drugs and more than 9000 gene perturbations. It allows easy execution of various analyses related to cancer drug sensitivity. With its large sample size and diverse drug range, CPADS offers a range of analysis methods, such as differential gene expression, gene correlation, pathway analysis, drug analysis and gene perturbation analysis. Additionally, it provides several visualization approaches. CPADS significantly aids physicians and researchers in exploring primary and secondary drug resistance at both gene and pathway levels. The integration of drug resistance and gene perturbation data also presents novel perspectives for identifying pivotal genes influencing drug resistance. Access CPADS at https://smuonco.shinyapps.io/CPADS/ or https://robinl-lab.com/CPADS.


Asunto(s)
Resistencia a Antineoplásicos , Internet , Neoplasias , Programas Informáticos , Humanos , Neoplasias/tratamiento farmacológico , Neoplasias/genética , Resistencia a Antineoplásicos/genética , Antineoplásicos/farmacología , Antineoplásicos/uso terapéutico , Biología Computacional/métodos , Bases de Datos Genéticas , Transcriptoma , Perfilación de la Expresión Génica/métodos
4.
J Immunol ; 212(2): 317-334, 2024 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-38054894

RESUMEN

The ancestors of chemokines originate in the most primitive of vertebrates, which has recently attracted great interest in the immune functions and the underlying mechanisms of fish chemokines. In the current study, we identified an evolutionarily conserved chemokine, CiCXCL13, from a teleost fish, grass carp. CiCXCL13 was characterized by a typical SCY (small cytokine CXC) domain and four cysteine residues (C34, C36, C61, C77), with the first two cysteines separated by a random amino acid residue, although it shared 24.2-54.8% identity with the counterparts from other vertebrates. CiCXCL13 was an inducible chemokine, whose expression was significantly upregulated in the immune tissues of grass carps after grass carp reovirus infection. CiCXCL13 could bind to the membrane of grass carp head kidney leukocytes and promote cell migration, NO release, and the expression of >15 inflammatory cytokines, including IL-1ß, TNF-α, IL-10 and TGF-ß1, thus regulating the inflammatory response. Mechanistically, CiCXCL13 interacted with its evolutionarily conserved receptor CiCXCR5 and activated the Akt-NF-κB and p38-AP-1 pathways, as well as a previously unrevealed p38-NF-κB pathway, to efficiently induce inflammatory cytokine expression, which was distinct from that reported in mammals. Zebrafish CXCL13 induced inflammatory cytokine expression through Akt, p38, NF-κB, and AP-1 as CiCXCL13. Meanwhile, the CiCXCL13-CiCXCR5 axis-mediated inflammatory activity was negatively shaped by grass carp atypical chemokine receptor 2 (CiACKR2). The present study is, to our knowledge, the first to comprehensively define the immune function of CXCL13 in inflammatory regulation and the underlying mechanism in teleosts, and it provides a valuable perspective on the evolution and biology of fish chemokines.


Asunto(s)
Carpas , Enfermedades de los Peces , Animales , FN-kappa B/metabolismo , Citocinas , Transducción de Señal , Proteínas Proto-Oncogénicas c-akt/metabolismo , Factor de Transcripción AP-1/metabolismo , Pez Cebra/metabolismo , Quimiocinas , Carpas/metabolismo , Proteínas de Peces/genética , Proteínas de Peces/metabolismo , Mamíferos/metabolismo
5.
Proc Natl Acad Sci U S A ; 120(51): e2300681120, 2023 Dec 19.
Artículo en Inglés | MEDLINE | ID: mdl-38100419

RESUMEN

Idiopathic normal pressure hydrocephalus (iNPH) is an enigmatic neurological disorder that develops after age 60 and is characterized by gait difficulty, dementia, and incontinence. Recently, we reported that heterozygous CWH43 deletions may cause iNPH. Here, we identify mutations affecting nine additional genes (AK9, RXFP2, PRKD1, HAVCR1, OTOG, MYO7A, NOTCH1, SPG11, and MYH13) that are statistically enriched among iNPH patients. The encoded proteins are all highly expressed in choroid plexus and ependymal cells, and most have been associated with cilia. Damaging mutations in AK9, which encodes an adenylate kinase, were detected in 9.6% of iNPH patients. Mice homozygous for an iNPH-associated AK9 mutation displayed normal cilia structure and number, but decreased cilia motility and beat frequency, communicating hydrocephalus, and balance impairment. AK9+/- mice displayed normal brain development and behavior until early adulthood, but subsequently developed communicating hydrocephalus. Together, our findings suggest that heterozygous mutations that impair ventricular epithelial function may contribute to iNPH.


Asunto(s)
Hidrocéfalo Normotenso , Hidrocefalia , Humanos , Ratones , Animales , Adulto , Persona de Mediana Edad , Hidrocéfalo Normotenso/genética , Hidrocéfalo Normotenso/complicaciones , Hidrocefalia/genética , Encéfalo , Plexo Coroideo , Mutación , Proteínas
6.
Plant Physiol ; 2024 Jun 14.
Artículo en Inglés | MEDLINE | ID: mdl-38875008

RESUMEN

Maintenance and homeostasis of the quiescent center (QC) in Arabidopsis (Arabidopsis thaliana) root apical meristems are critical for stem cell organization and root development. Despite great progress in relevant research, the molecular mechanisms that determine the root stem cell fate and QC still need further exploration. In Arabidopsis, SUPPRESSOR OF FRIGIDA 4 (SUF4) encodes a C2H2-type zinc finger protein that represses flowering by transcriptional activation of FLOWERING LOCUS C (FLC) through the FRIGIDA (FRI) pathway, and EARLY BOLTING IN SHORT DAYS (EBS) is a bivalent histone reader that prevents premature flowering. Here, we found that SUF4 directly interacts with EBS in vivo and in vitro. Loss of function of SUF4 and/or EBS resulted in disorganization of the QC, aberrant cell division, and stunted root growth. RNA-seq and reverse transcription quantitative real-time polymerase chain reaction analysis revealed that SUF4 and EBS coregulate many root development-related genes. A series of biochemical analyses demonstrated that SUF4 directly binds to the promoter of SCARECROW (SCR), which encodes a key regulator of root development. Chromatin immunoprecipitation assay indicated that both SUF4 and EBS are recruited to the SCR locus in an interdependent manner to promote H3K4me3 levels and suppress H3K27me3 levels, thereby activating the expression of SCR. These findings improve our understanding of the function of SUF4 and EBS and provide insights into the molecular mechanism that couples a transcription factor and a histone methylation reader to modulate QC specification and root development in Arabidopsis.

7.
PLoS Comput Biol ; 20(3): e1011247, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38427689

RESUMEN

The advancements in next-generation sequencing have made it possible to effectively detect somatic mutations, which has led to the development of personalized neoantigen cancer vaccines that are tailored to the unique variants found in a patient's cancer. These vaccines can provide significant clinical benefit by leveraging the patient's immune response to eliminate malignant cells. However, determining the optimal vaccine dose for each patient is a challenge due to the heterogeneity of tumors. To address this challenge, we formulate a mathematical dose optimization problem based on a previous mathematical model that encompasses the immune response cascade produced by the vaccine in a patient. We propose an optimization approach to identify the optimal personalized vaccine doses, considering a fixed vaccination schedule, while simultaneously minimizing the overall number of tumor and activated T cells. To validate our approach, we perform in silico experiments on six real-world clinical trial patients with advanced melanoma. We compare the results of applying an optimal vaccine dose to those of a suboptimal dose (the dose used in the clinical trial and its deviations). Our simulations reveal that an optimal vaccine regimen of higher initial doses and lower final doses may lead to a reduction in tumor size for certain patients. Our mathematical dose optimization offers a promising approach to determining an optimal vaccine dose for each patient and improving clinical outcomes.


Asunto(s)
Vacunas contra el Cáncer , Melanoma , Humanos , Melanoma/genética , Vacunas contra el Cáncer/genética , Antígenos de Neoplasias/genética , Adyuvantes Inmunológicos , Péptidos
8.
PLoS Comput Biol ; 20(5): e1012024, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38717988

RESUMEN

The activation levels of biologically significant gene sets are emerging tumor molecular markers and play an irreplaceable role in the tumor research field; however, web-based tools for prognostic analyses using it as a tumor molecular marker remain scarce. We developed a web-based tool PESSA for survival analysis using gene set activation levels. All data analyses were implemented via R. Activation levels of The Molecular Signatures Database (MSigDB) gene sets were assessed using the single sample gene set enrichment analysis (ssGSEA) method based on data from the Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), The European Genome-phenome Archive (EGA) and supplementary tables of articles. PESSA was used to perform median and optimal cut-off dichotomous grouping of ssGSEA scores for each dataset, relying on the survival and survminer packages for survival analysis and visualisation. PESSA is an open-access web tool for visualizing the results of tumor prognostic analyses using gene set activation levels. A total of 238 datasets from the GEO, TCGA, EGA, and supplementary tables of articles; covering 51 cancer types and 13 survival outcome types; and 13,434 tumor-related gene sets are obtained from MSigDB for pre-grouping. Users can obtain the results, including Kaplan-Meier analyses based on the median and optimal cut-off values and accompanying visualization plots and the Cox regression analyses of dichotomous and continuous variables, by selecting the gene set markers of interest. PESSA (https://smuonco.shinyapps.io/PESSA/ OR http://robinl-lab.com/PESSA) is a large-scale web-based tumor survival analysis tool covering a large amount of data that creatively uses predefined gene set activation levels as molecular markers of tumors.


Asunto(s)
Biomarcadores de Tumor , Biología Computacional , Bases de Datos Genéticas , Internet , Neoplasias , Programas Informáticos , Humanos , Neoplasias/genética , Neoplasias/mortalidad , Análisis de Supervivencia , Biomarcadores de Tumor/genética , Biomarcadores de Tumor/metabolismo , Biología Computacional/métodos , Pronóstico , Perfilación de la Expresión Génica/métodos , Regulación Neoplásica de la Expresión Génica/genética
9.
Chem Rev ; 123(7): 3443-3492, 2023 Apr 12.
Artículo en Inglés | MEDLINE | ID: mdl-36802540

RESUMEN

This paper reviews recent studies on the preparation of two-dimensional (2D) metal nanostructures, particularly nanosheets. As metal often exists in the high-symmetry crystal phase, such as face centered cubic structures, reducing the symmetry is often needed for the formation of low-dimensional nanostructures. Recent advances in characterization and theory allow for a deeper understanding of the formation of 2D nanostructures. This Review firstly describes the relevant theoretical framework to help the experimentalists understand chemical driving forces for the synthesis of 2D metal nanostructures, followed by examples on the shape control of different metals. Recent applications of 2D metal nanostructures, including catalysis, bioimaging, plasmonics, and sensing, are discussed. We end the Review with a summary and outlook of the challenges and opportunities in the design, synthesis, and application of 2D metal nanostructures.

10.
Exp Cell Res ; 437(1): 114008, 2024 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-38499143

RESUMEN

Hepatocytes are responsible for maintaining a stable blood glucose concentration during periods of nutrient scarcity. The breakdown of glycogen and de novo synthesis of glucose are crucial metabolic pathways deeply interlinked with lipid metabolism. Alterations in these pathways are often associated with metabolic diseases with serious clinical implications. Studying energy metabolism in human cells is challenging. Primary hepatocytes are still considered the golden standard for in vitro studies and have been instrumental in elucidating key aspects of energy metabolism found in vivo. As a result of several limitations posed by using primary cells, a multitude of alternative hepatocyte cellular models emerged as potential substitutes. Yet, there remains a lack of clarity regarding the precise applications for which these models accurately reflect the metabolic competence of primary hepatocytes. In this study, we compared primary hepatocytes, stem cell-derived hepatocytes, adult donor-derived liver organoids, immortalized Upcyte-hepatocytes and the hepatoma cell line HepG2s in their response to a glucose production challenge. We observed the highest net glucose production in primary hepatocytes, followed by organoids, stem-cell derived hepatocytes, Upcyte-hepatocytes and HepG2s. Glucogenic gene induction was observed in all tested models, as indicated by an increase in G6PC and PCK1 expression. Lipidomic analysis revealed considerable differences across the models, with organoids showing the closest similarity to primary hepatocytes in the common lipidome, comprising 347 lipid species across 19 classes. Changes in lipid profiles as a result of the glucose production challenge showed a variety of, and in some cases opposite, trends when compared to primary hepatocytes.


Asunto(s)
Carcinoma Hepatocelular , Glucosa , Humanos , Glucosa/metabolismo , Hepatocitos/metabolismo , Carcinoma Hepatocelular/metabolismo , Línea Celular , Metabolismo de los Lípidos , Lípidos , Hígado/metabolismo
11.
Nucleic Acids Res ; 51(17): e90, 2023 09 22.
Artículo en Inglés | MEDLINE | ID: mdl-37562941

RESUMEN

The detection of nucleic acid sequences in parallel with the discrimination of single nucleotide variations (SNVs) is critical for research and clinical applications. A few limitations make the detection technically challenging, such as too small variation in probe-hybridization energy caused by SNVs, the non-specific amplification of false nucleic acid fragments and the few options of dyes limited by spectral overlaps. To circumvent these limitations, we developed a single-molecule nucleic acid detection assay without amplification or fluorescence termed THREF (hybridization-induced tandem DNA hairpin refolding failure) based on multiplexed magnetic tweezers. THREF can detect DNA and RNA sequences at femtomolar concentrations within 30 min, monitor multiple probes in parallel, quantify the expression level of miR-122 in patient tissues, discriminate SNVs including the hard-to-detect G-U or T-G wobble mutations and reuse the probes to save the cost. In our demonstrative detections using mock clinic samples, we profiled the let-7 family microRNAs in serum and genotyped SARS-CoV-2 strains in saliva. Overall, the THREF assay can discriminate SNVs with the advantages of high sensitivity, ultra-specificity, multiplexing, reusability, sample hands-free and robustness.


Asunto(s)
Técnicas Genéticas , Polimorfismo Genético , ARN , Humanos , COVID-19/diagnóstico , ADN/genética , Mutación , SARS-CoV-2/genética , ARN/análisis
12.
Nano Lett ; 24(18): 5639-5646, 2024 May 08.
Artículo en Inglés | MEDLINE | ID: mdl-38668743

RESUMEN

Structural complexity brings a huge challenge to the analysis of sugar chains. As a single-molecule sensor, nanopores have the potential to provide fingerprint information on saccharides. Traditionally, direct single-molecule saccharide detection with nanopores is hampered by their small size and weak affinity. Here, a carbon nitride nanopore device is developed to discern two types of trisaccharide molecules (LeApN and SLeCpN) with minor structural differences. The resolution of LeApN and SLeCpN in the mixture reaches 0.98, which has never been achieved in solid-state nanopores so far. Monosaccharide (GlcNAcpN) and disaccharide (LacNAcpN) can also be discriminated using this system, indicating that the versatile carbon nitride nanopores possess a monosaccharide-level resolution. This study demonstrates that the carbon nitride nanopores have the potential for conducting structure analysis on single-molecule saccharides.

13.
Nano Lett ; 24(9): 2931-2938, 2024 Mar 06.
Artículo en Inglés | MEDLINE | ID: mdl-38377049

RESUMEN

Plasmon-induced hot-electron transfer at the metallic nanoparticle/semiconductor interface is the basis of plasmon-enhanced photocatalysis and energy harvesting. However, limited by the nanoscale size of hot spots and femtosecond time scale of hot-electron transfer, direct observation is still challenging. Herein, by using spatiotemporal-resolved photoemission electron microscopy with a two-color pump-probe beamline, we directly observed such a process with a concise system, the Au nanoparticle/monolayer transition-metal dichalcogenide (TMD) interface. The ultrafast hot-electron transfer from Au nanoparticles to monolayer TMDs and the plasmon-enhanced transfer process were directly measured and verified through an in situ comparison with the Au film/TMD interface and free TMDs. The lifetime at the Au nanoparticle/MoSe2 interface decreased from 410 to 42 fs, while the photoemission intensities exhibited a 27-fold increase compared to free MoSe2. We also measured the evolution of hot electrons in the energy distributions, indicating the hot-electron injection and decay happened in an ultrafast time scale of ∼50 fs without observable electron cooling.

14.
J Mol Cell Cardiol ; 190: 62-75, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38583797

RESUMEN

Intimal hyperplasia is a complicated pathophysiological phenomenon attributable to in-stent restenosis, and the underlying mechanism remains unclear. Interleukin enhancer-binding factor 3 (ILF3), a double-stranded RNA-binding protein involved in regulating mRNA stability, has been recently demonstrated to assume a crucial role in cardiovascular disease; nevertheless, its impact on intimal hyperplasia remains unknown. In current study, we used samples of human restenotic arteries and rodent models of intimal hyperplasia, we found that vascular smooth muscle cell (VSMC) ILF3 expression was markedly elevated in human restenotic arteries and murine ligated carotid arteries. SMC-specific ILF3 knockout mice significantly suppressed injury induced neointimal formation. In vitro, platelet-derived growth factor type BB (PDGF-BB) treatment elevated the level of VSMC ILF3 in a dose- and time-dependent manner. ILF3 silencing markedly inhibited PDGF-BB-induced phenotype switching, proliferation, and migration in VSMCs. Transcriptome sequencing and RNA immunoprecipitation sequencing depicted that ILF3 maintained its stability upon binding to the mRNA of the high-mobility group box 1 protein (HMGB1), thereby exerting an inhibitory effect on the transcription of dual specificity phosphatase 16 (DUSP16) through enhanced phosphorylation of signal transducer and activator of transcription 3 (STAT3). Therefore, the results both in vitro and in vivo indicated that the loss of ILF3 in VSMC ameliorated neointimal hyperplasia by regulating the STAT3/DUSP16 axis through the degradation of HMGB1 mRNA. Our findings revealed that vascular injury activates VSMC ILF3, which in turn promotes intima formation. Consequently, targeting specific VSMC ILF3 may present a potential therapeutic strategy for ameliorating cardiovascular restenosis.


Asunto(s)
Proteína HMGB1 , Hiperplasia , Ratones Noqueados , Músculo Liso Vascular , Miocitos del Músculo Liso , Proteínas del Factor Nuclear 90 , Estabilidad del ARN , Factor de Transcripción STAT3 , Túnica Íntima , Animales , Humanos , Masculino , Ratones , Movimiento Celular , Proliferación Celular , Modelos Animales de Enfermedad , Regulación de la Expresión Génica , Proteína HMGB1/metabolismo , Proteína HMGB1/genética , Músculo Liso Vascular/metabolismo , Músculo Liso Vascular/patología , Miocitos del Músculo Liso/metabolismo , Neointima/metabolismo , Neointima/patología , Proteínas del Factor Nuclear 90/metabolismo , Proteínas del Factor Nuclear 90/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo , Transducción de Señal , Factor de Transcripción STAT3/metabolismo , Túnica Íntima/metabolismo , Túnica Íntima/patología
15.
BMC Bioinformatics ; 25(1): 139, 2024 Mar 29.
Artículo en Inglés | MEDLINE | ID: mdl-38553698

RESUMEN

BACKGROUND: MicroRNA (miRNA) has been shown to play a key role in the occurrence and progression of diseases, making uncovering miRNA-disease associations vital for disease prevention and therapy. However, traditional laboratory methods for detecting these associations are slow, strenuous, expensive, and uncertain. Although numerous advanced algorithms have emerged, it is still a challenge to develop more effective methods to explore underlying miRNA-disease associations. RESULTS: In the study, we designed a novel approach on the basis of deep autoencoder and combined feature representation (DAE-CFR) to predict possible miRNA-disease associations. We began by creating integrated similarity matrices of miRNAs and diseases, performing a logistic function transformation, balancing positive and negative samples with k-means clustering, and constructing training samples. Then, deep autoencoder was used to extract low-dimensional feature from two kinds of feature representations for miRNAs and diseases, namely, original association information-based and similarity information-based. Next, we combined the resulting features for each miRNA-disease pair and used a logistic regression (LR) classifier to infer all unknown miRNA-disease interactions. Under five and tenfold cross-validation (CV) frameworks, DAE-CFR not only outperformed six popular algorithms and nine classifiers, but also demonstrated superior performance on an additional dataset. Furthermore, case studies on three diseases (myocardial infarction, hypertension and stroke) confirmed the validity of DAE-CFR in practice. CONCLUSIONS: DAE-CFR achieved outstanding performance in predicting miRNA-disease associations and can provide evidence to inform biological experiments and clinical therapy.


Asunto(s)
MicroARNs , Humanos , MicroARNs/genética , Biología Computacional/métodos , Algoritmos , Predisposición Genética a la Enfermedad
16.
Carcinogenesis ; 45(4): 262-273, 2024 Apr 12.
Artículo en Inglés | MEDLINE | ID: mdl-37997385

RESUMEN

OBJECTIVES: There are three major subtypes of breast cancer, ER+, HER2+ and triple-negative breast cancer (TNBC), namely ER-, PR-, HER2-. TNBC is the most aggressive breast cancer with poor prognosis and no target drug up to now. Actinomycin D (ActD) is a bioactive metabolite of marine bacteria that has been reported to have antitumor activity. The aim of study is to investigate whether ActD has a synergetic effect on TNBC with Doxorubicin (Dox), the major chemotherapeutic drug for TNBC, and explore the underlying mechanism. METHODS: TNBC cell lines HCC1937, MDA-MB-436 and nude mice were used in the study. Drug synergy determination, LDH assay, MMP assay, Hoechst 33342 staining, Flow cytometry, Flexible docking and CESTA assay were carried out. The expression of proteins associated with apoptosis was checked by Western blot and siRNA experiments were performed to investigate the role of P53 and PUMA induced by drugs. RESULTS: There was much higher apoptosis rate of cells in the ActD + Dox group than that in ActD group or Dox group. Expression of MDM2 and BCL-2 was reduced while expression of P53, PUMA and BAX were increased in the groups treated with ActD + Dox or Dox compared to the control group. Furthermore, P53 siRNA or PUMA siRNA tremendously abrogated the cell apoptosis in the groups treated by ActD, Dox and ActD + Dox. Flexible docking and CESTA showed that ActD can bind MDM2. CONCLUSIONS: ActD had a synergetic effect on TNBC with Dox via P53-dependent apoptosis and it may be a new choice for treatment of TNBC.


Asunto(s)
Neoplasias de la Mama Triple Negativas , Ratones , Humanos , Animales , Neoplasias de la Mama Triple Negativas/genética , Dactinomicina/farmacología , Dactinomicina/metabolismo , Dactinomicina/uso terapéutico , Proteína p53 Supresora de Tumor/genética , Proteína p53 Supresora de Tumor/metabolismo , Ratones Desnudos , Proteínas Reguladoras de la Apoptosis , Línea Celular Tumoral , Doxorrubicina/farmacología , Apoptosis , ARN Interferente Pequeño
17.
J Cell Mol Med ; 28(1): e18030, 2024 01.
Artículo en Inglés | MEDLINE | ID: mdl-37929884

RESUMEN

Acetylshikonin (AS) is an active component of Lithospermum erythrorhizon Sieb. et Zucc that exhibits activity against various cancers; however, the underlying mechanisms of AS against oesophageal squamous carcinoma (ESCC) need to be elusive. The research explores the anti-cancer role and potential mechanism of AS on ESCC in vitro and in vivo, providing evidences for AS treatment against ESCC. In this study, we firstly demonstrated that AS treatment effectively inhibits cell viability and proliferation of ESCC cells. In addition, AS significantly induces G1/S phage arrest and promotes apoptosis in ESCC cell lines. Further studies reveal that AS induces ER stress, as observed by dose- and time-dependently increased expression of BIP, PDI, PERK, phosphorylation of eIF2α , CHOP and splicing of XBP1. CHOP knockdown or PERK inhibition markedly rescue cell apoptosis induced by AS. Moreover, AS treatment significantly inhibits ESCC xenograft growth in nude mice. Elevated expression of BIP and CHOP is also observed in xenograft tumours. Taken together, AS inhibits proliferation and induces apoptosis through ER stress-activated PERK/eIF2α /CHOP pathway in ESCC, which indicates AS represents a promising candidate for ESCC treatment.


Asunto(s)
Antraquinonas , Neoplasias Esofágicas , Carcinoma de Células Escamosas de Esófago , Ratones , Animales , Humanos , eIF-2 Quinasa/metabolismo , Factor 2 Eucariótico de Iniciación/metabolismo , Ratones Desnudos , Estrés del Retículo Endoplásmico , Apoptosis , Factor de Transcripción CHOP/metabolismo
18.
Infect Immun ; 92(3): e0056022, 2024 Mar 12.
Artículo en Inglés | MEDLINE | ID: mdl-38363133

RESUMEN

The Gram-negative bacterium Coxiella burnetii is the causative agent of query fever in humans and coxiellosis in livestock. C. burnetii infects a variety of cell types, tissues, and animal species including mammals and arthropods, but there is much left to be understood about the molecular mechanisms at play during infection in distinct species. Human stimulator of interferon genes (STING) induces an innate immune response through the induction of type I interferons (IFNs), and IFN promotes or suppresses C. burnetii replication, depending on tissue type. Drosophila melanogaster contains a functional STING ortholog (Sting) which activates NF-κB signaling and autophagy. Here, we sought to address the role of D. melanogaster Sting during C. burnetii infection to uncover how Sting regulates C. burnetii infection in flies. We show that Sting-null flies exhibit higher mortality and reduced induction of antimicrobial peptides following C. burnetii infection compared to control flies. Additionally, Sting-null flies induce lower levels of oxidative stress genes during infection, but the provision of N-acetyl-cysteine (NAC) in food rescues Sting-null host survival. Lastly, we find that reactive oxygen species levels during C. burnetii infection are higher in Drosophila S2 cells knocked down for Sting compared to control cells. Our results show that at the host level, NAC provides protection against C. burnetii infection in the absence of Sting, thus establishing a role for Sting in protection against oxidative stress during C. burnetii infection.


Asunto(s)
Coxiella burnetii , Fiebre Q , Animales , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , FN-kappa B/metabolismo , Fiebre Q/microbiología , Especies Reactivas de Oxígeno/metabolismo
19.
J Cell Physiol ; 2024 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-38949237

RESUMEN

Cancer-associated fibroblasts (CAFs) are a major cellular component in the tumor microenvironment and have been shown to exhibit protumorigenic effects in hepatocellular carcinoma (HCC). This study aimed to delve into the mechanisms underlying the tumor-promoting effects of CAFs in HCC. Small RNA sequencing was conducted to screen differential expressed microRNAs in exosomes derived from CAFs and normal fibroblasts (NFs). The miR-92a-3p expression was then measured using reverse transcriptase quantitative real-time PCR in CAFs, NFs, CAFs-derived exosomes (CAFs-Exo), and NF-derived exosomes (NFs-Exo). Compared to NFs or NF-Exo, CAFs and CAFs-Exo significantly promoted HCC cell proliferation, migration, and stemness. Additionally, compared to NFs or NF-Exo, miR-92a-3p level was notably higher in CAFs and CAFs-Exo, respectively. Exosomal miR-92a-3p was found to enhance HCC cell proliferation, migration, and stemness. Meanwhile, AXIN1 was targeted by miR-92a-3p. Exosomal miR-92a-3p could activate ß-catenin/CD44 signaling in HCC cells by inhibiting AXIN1 messenger RNA. Furthermore, in vivo studies verified that exosomal miR-92a-3p notably promoted tumor growth and stemness through targeting AXIN1/ß-catenin axis. Collectively, CAFs secreted exosomal miR-92a-3p was capable of promoting growth and stemness in HCC through activation of Wnt/ß-catenin signaling pathway by suppressing AXIN1. Therefore, targeting CAFs-derived miR-92a-3p may be a potential strategy for treating HCC.

20.
J Am Chem Soc ; 2024 May 31.
Artículo en Inglés | MEDLINE | ID: mdl-38820244

RESUMEN

Oxygen evolution reaction (OER) takes place in various types of electrochemical devices that are pivotal for the conversion and storage of renewable energy. This paper describes a strategy in the design of solid-state structures of OER electrocatalysts through controlling the cation substitution on the active metal site and consequently valence band center position of site-mixed Y2(YxRu1-x)2O7-δ pyrochlore to achieve high catalytic activity. We found that partially replacing the B-site Ru4+ cation with A-site Y3+ in pyrochlore-structured Y2Ru2O7-δ modifies the oxidation state of B-site Ru from 4+ to 5+, as observed by electron paramagnetic resonance (EPR) spectroscopy but does not continuously increase the oxygen vacancy concentration in these oxygen substoichiometric compositions, as quantified by thermogravimetric analysis (TGA) decomposition studies. We found the increased Ru oxidation state leads to a downshift in valence band center. X-ray photoelectron spectroscopy (XPS) analysis was performed to quantitatively determine the optimal band center to be ∼1.27 eV below the Fermi energy level based on the analysis of the valence band edge of these Ru-based Y2(YxRu1-x)2O7-δ OER electrocatalysts. This work highlights that defect engineering can be a practical, effective approach to the optimization of oxidation state and electronic band center for high OER catalytic performance in a quantitative manner.

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