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1.
PLoS Genet ; 20(6): e1011309, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38885192

RESUMEN

PLK1 (Polo-like kinase 1) plays a critical role in the progression of lung adenocarcinoma (LUAD). Recent studies have unveiled that targeting PLK1 improves the efficacy of immunotherapy, highlighting its important role in the regulation of tumor immunity. Nevertheless, our understanding of the intricate interplay between PLK1 and the tumor microenvironment (TME) remains incomplete. Here, using genetically engineered mouse model and single-cell RNA-seq analysis, we report that PLK1 promotes an immunosuppressive TME in LUAD, characterized with enhanced M2 polarization of tumor associated macrophages (TAM) and dampened antigen presentation process. Mechanistically, elevated PLK1 coincides with increased secretion of CXCL2 cytokine, which promotes M2 polarization of TAM and diminishes expression of class II major histocompatibility complex (MHC-II) in professional antigen-presenting cells. Furthermore, PLK1 negatively regulates MHC-II expression in cancer cells, which has been shown to be associated with compromised tumor immunity and unfavorable patient outcomes. Taken together, our results reveal PLK1 as a novel modulator of TME in LUAD and provide possible therapeutic interventions.


Asunto(s)
Adenocarcinoma del Pulmón , Proteínas de Ciclo Celular , Neoplasias Pulmonares , Quinasa Tipo Polo 1 , Proteínas Serina-Treonina Quinasas , Proteínas Proto-Oncogénicas , Análisis de la Célula Individual , Microambiente Tumoral , Animales , Humanos , Ratones , Adenocarcinoma del Pulmón/genética , Adenocarcinoma del Pulmón/inmunología , Adenocarcinoma del Pulmón/patología , Presentación de Antígeno/genética , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Línea Celular Tumoral , Quimiocina CXCL2/genética , Quimiocina CXCL2/metabolismo , Regulación Neoplásica de la Expresión Génica , Antígenos de Histocompatibilidad Clase II/genética , Antígenos de Histocompatibilidad Clase II/metabolismo , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/inmunología , Neoplasias Pulmonares/patología , Proteínas Serina-Treonina Quinasas/genética , Proteínas Serina-Treonina Quinasas/metabolismo , Proteínas Proto-Oncogénicas/genética , Proteínas Proto-Oncogénicas/metabolismo , Microambiente Tumoral/inmunología , Microambiente Tumoral/genética , Macrófagos Asociados a Tumores/inmunología , Macrófagos Asociados a Tumores/metabolismo
2.
Proc Natl Acad Sci U S A ; 119(28): e2119518119, 2022 07 12.
Artículo en Inglés | MEDLINE | ID: mdl-35867755

RESUMEN

Early B cell factor 1 (EBF1) is a transcriptional factor with a variety of roles in cell differentiation and metabolism. However, the functional roles of EBF1 in tumorigenesis remain elusive. Here, we demonstrate that EBF1 is highly expressed in triple-negative breast cancer (TNBC). Furthermore, EBF1 has a pivotal role in the tumorigenicity and progression of TNBC. Moreover, we found that depletion of EBF1 induces extensive cell mitophagy and inhibits tumor growth. Genome-wide mapping of the EBF1 transcriptional regulatory network revealed that EBF1 drives TNBC tumorigenicity by assembling a transcriptional complex with HIF1α that fine-tunes the expression of HIF1α targets via suppression of p300 activity. EBF1 therefore holds HIF1α activity in check to avert extensive mitophagy-induced cell death. Our findings reveal a key function for EBF1 as a master regulator of mitochondria homeostasis in TNBC and indicate that targeting this pathway may offer alternative treatment strategies for this aggressive subtype of breast cancer.


Asunto(s)
Subunidad alfa del Factor 1 Inducible por Hipoxia , Transactivadores , Neoplasias de la Mama Triple Negativas , Carcinogénesis/genética , Línea Celular Tumoral , Proliferación Celular , Regulación Neoplásica de la Expresión Génica , Humanos , Subunidad alfa del Factor 1 Inducible por Hipoxia/metabolismo , Transducción de Señal , Transactivadores/genética , Transactivadores/metabolismo , Neoplasias de la Mama Triple Negativas/metabolismo , Neoplasias de la Mama Triple Negativas/patología
3.
BMC Genomics ; 25(1): 911, 2024 Sep 30.
Artículo en Inglés | MEDLINE | ID: mdl-39350018

RESUMEN

BACKGROUND: Guinea pigs exhibit numerous physiological similarities to humans, yet the details of their preimplantation embryonic development remain largely unexplored. RESULTS: To address this, we conducted single-cell sequencing on the transcriptomes of cells isolated from the zygote stage through preimplantation stages in guinea pigs. This study identified seven distinct cell types within guinea pig preimplantation embryos and pinpointed the timing of zygotic gene activation (ZGA). Trajectory analysis revealed a bifurcation into two lineage-specific branches, accompanied by alterations in specific pathways, including oxidative phosphorylation and vascular endothelial growth factor (VEGF). Additionally, co-expressed gene network analysis highlighted the most enriched functional modules for the epiblast (EPI), primitive endoderm (PrE), and inner cell mass (ICM). Finally, we compared the similarities and differences between human and guinea pig epiblasts (EPIs). CONCLUSION: This study systematically constructs a cell atlas of guinea pig preimplantation embryonic development, offering fresh insights into mammalian embryonic development and providing alternative experimental models for studying human embryonic development.


Asunto(s)
Blastocisto , Desarrollo Embrionario , Análisis de la Célula Individual , Animales , Cobayas , Humanos , Blastocisto/metabolismo , Blastocisto/citología , Estratos Germinativos/metabolismo , Estratos Germinativos/citología , Femenino , Regulación del Desarrollo de la Expresión Génica , Transcriptoma , Redes Reguladoras de Genes
4.
J Pharmacol Exp Ther ; 2024 Oct 08.
Artículo en Inglés | MEDLINE | ID: mdl-39379144

RESUMEN

Androgen deprivation is the standard treatment for prostate cancer (PCa) patients. However, the disease eventually progresses as castration-resistant PCa (CRPC). Enzalutamide, an AR inhibitor, is a typical drug to treating CRPC and due to continuous reliance on the drug, can lead to Enzalutamide-resistance (ENZ-r). This highlights the necessity for developing novel therapeutic targets to combat the gain of resistance. Metformin has been recently investigated for its potential anti-tumorigenic effects in many cancer types. In this study, we used enzalutamide and metformin in combination to explore the possible rescued efficacy of enzalutamide in the treatment of ENZ-r CRPC. We first tested the effects of this combination treatment on cell viability, drug synergy, and cell proliferation in ENZ-r CRPC cell lines. After combination treatment, we observed a decrease in cell proliferation and viability as well as a synergistic effect of both enzalutamide and metformin in vitro Following these results, we sought to explore how combination treatment effected mitochondrial fitness utilizing mitochondrial stress test analysis and mitochondrial membrane potential (MMP) shifts due to metformin's action in inhibiting Complex I of oxidative phosphorylation. We employed 2 different strategies of in vivo testing using 22Rv1 and LuCaP35CR xenograft models. Finally, RNA sequencing revealed a potential link in the downregulation of Ras/MAPK signaling following combination treatment. Significance Statement Increasing evidence suggests that oxidative phosphorylation might play a critical role in the development of resistance to cancer therapy. We showed that targeting oxidative phosphorylation with metformin can enhance the efficacy of enzalutamide in castration-resistant prostate cancer in vitro.

5.
J Transl Med ; 22(1): 710, 2024 Jul 30.
Artículo en Inglés | MEDLINE | ID: mdl-39080755

RESUMEN

BACKGROUND: Myopia is one of the most common eye diseases in children and adolescents worldwide, and scleral remodeling plays a role in myopia progression. However, the identity of the initiating factors and signaling pathways that induce myopia-associated scleral remodeling is still unclear. This study aimed to identify biomarkers of scleral remodeling to elucidate the pathogenesis of myopia. METHODS: The gene expression omnibus (GEO) and comparative toxicogenomics database (CTD) mining were used to identify the miRNA-mRNA regulatory network related to scleral remodeling in myopia. Real-time quantitative PCR (RT-qPCR), Western blot, immunofluorescence, H&E staining, Masson staining, and flow cytometry were used to detect the changes in the FOXO signaling pathway, fibrosis, apoptosis, cell cycle, and other related factors in scleral remodeling. RESULTS: miR-15b-5p/miR-379-3p can regulate the FOXO signaling pathway. Confirmatory studies confirmed that the axial length of the eye was significantly increased, the scleral thickness was thinner, the levels of miR-15b-5p, miR-379-3p, PTEN, p-PTEN, FOXO3a, cyclin-dependent kinase (CDK) inhibitor 1B (CDKN1B) were increased, and the levels of IGF1R were decreased in Len-induced myopia (LIM) group. CDK2, cyclin D1 (CCND1), and cell cycle block assessed by flow cytometry indicated G1/S cell cycle arrest in myopic sclera. The increase in BAX level and the decrease in BCL-2 level indicated enhanced apoptosis of the myopic sclera. In addition, we found that the levels of transforming growth factor-ß1 (TGF-ß1), collagen type 1 (COL-1), and α-smooth muscle actin (α-SMA) were decreased, suggesting scleral remodeling occurred in myopia. CONCLUSIONS: miR-15b-5p/miR-379-3p can regulate the scleral cell cycle and apoptosis through the IGF1R/PTEN/FOXO signaling pathway, thereby promoting scleral remodeling in myopia progression.


Asunto(s)
Apoptosis , Ciclo Celular , Factores de Transcripción Forkhead , MicroARNs , Miopía , Esclerótica , Transducción de Señal , Animales , Apoptosis/genética , Secuencia de Bases , Ciclo Celular/genética , Modelos Animales de Enfermedad , Factores de Transcripción Forkhead/metabolismo , Factores de Transcripción Forkhead/genética , MicroARNs/genética , MicroARNs/metabolismo , Miopía/genética , Miopía/patología , Miopía/metabolismo , Esclerótica/patología , Esclerótica/metabolismo
6.
J Transl Med ; 22(1): 511, 2024 May 28.
Artículo en Inglés | MEDLINE | ID: mdl-38807184

RESUMEN

BACKGROUND: Myopia is one of the eye diseases that can damage the vision of young people. This study aimed to explore the protective role of miR-92b-3p against DNA damage and apoptosis in retinal tissues of negative lens-induced myopic (LIM) guinea pigs by targeting BTG2. METHODS: Biometric measurements of ocular parameters, flash electroretinogram (FERG), and retinal thickness (RT) were performed after miR-92b-3p intravitreal injection in LIM guinea pigs. The apoptotic rate was detected by Annexin V-FITC/PI double staining, and the change in mitochondrial membrane potential was measured by JC-1 staining. Retinal apoptosis and expression of p53, BTG2, and CDK2 were explored by TdT-mediated dUTP-biotin nick labeling (TUNEL) and immunofluorescence staining assays, respectively. BTG2 and its upstream and downstream molecules at gene and protein levels in retinal tissues were measured by real-time quantitative PCR (qPCR) and Western blotting. RESULTS: Compared with normal controls (NC), the ocular axial length of LIM guinea pig significantly increased, whereas refraction decreased. Meanwhile, dMax-a and -b wave amplitudes of ERG declined, retinal thickness was decreased, the number of apoptotic cells and apoptotic rate in LIM eyes was exaggerated, and the mitochondrial membrane potential significantly decreased. In addition, results of qPCR and Western blot assays showed that the expression levels of p53, BTG2, CDK2, and BAX in LIM guinea pigs were higher than the levels of the NC group, whereas the BCL-2 expression level was decreased. By contrast, the miR-92b-3p intravitreal injection in LIM guinea pigs could significantly inhibit axial elongation, alleviate DNA damage and apoptosis, and thus protect guinea pigs against myopia. CONCLUSION: In conclusion, p53 and BTG2 were activated in the retinal tissue of myopic guinea pigs, and the activated BTG2 could elevate the expression of CDK2 and BAX, and attenuate the expression of BCL-2, which in turn promote apoptosis and eventually lead to retinal thinning and impaired visual function in myopic guinea pigs. The miR-92b-3p intravitreal injection can attenuate the elongation of ocular length and retinal thickness, and inhibit the CDK2, BAX, and p53 expression by targeting BTG2, thereby ameliorating DNA damage and apoptosis in LIM guinea pigs and protecting ocular tissues.


Asunto(s)
Apoptosis , Daño del ADN , MicroARNs , Miopía , Retina , Animales , Cobayas , Modelos Animales de Enfermedad , Electrorretinografía , Proteínas Inmediatas-Precoces/metabolismo , Proteínas Inmediatas-Precoces/genética , Potencial de la Membrana Mitocondrial , MicroARNs/genética , MicroARNs/metabolismo , Miopía/metabolismo , Miopía/genética , Miopía/patología , Retina/patología , Retina/metabolismo , Proteína p53 Supresora de Tumor/metabolismo , Proteínas Supresoras de Tumor/metabolismo , Proteínas Supresoras de Tumor/genética
7.
Int J Med Sci ; 21(9): 1589-1603, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-39006849

RESUMEN

Myopia represents a significant public health concern worldwide, particularly affecting the ocular health of children and adolescents. The escalating prevalence of myopia in recent years underscores its urgency as a health issue among this demographic. Research indicates a profound connection between the onset of myopia, inflammatory processes and fibrosis. Individuals with inflammatory conditions like allergic conjunctivitis, choroiditis, systemic lupus erythematosus, and diabetes exhibit a heightened susceptibility to myopia. Conversely, myopic patients are at an increased risk of developing ocular inflammatory disorders, notably idiopathic multifocal choroiditis. We postulate that the expression of inflammatory markers, including NF-κB, TGF-ß, IL-1ß, IL-6, IL-8, and TNF-α, may contribute to the chronic inflammatory state observed in myopia. This paper highlights a substantial correlation between myopia and inflammation, suggesting the potential efficacy of anti-inflammatory agents in managing inflammation and slowing myopia progression.


Asunto(s)
Inflamación , Miopía , Niño , Humanos , Antiinflamatorios/uso terapéutico , Citocinas/metabolismo , Progresión de la Enfermedad , Inflamación/patología , Miopía/epidemiología , Miopía/metabolismo , Miopía/patología
8.
Proc Natl Acad Sci U S A ; 118(35)2021 08 31.
Artículo en Inglés | MEDLINE | ID: mdl-34446548

RESUMEN

Nonlinear differential equations model diverse phenomena but are notoriously difficult to solve. While there has been extensive previous work on efficient quantum algorithms for linear differential equations, the linearity of quantum mechanics has limited analogous progress for the nonlinear case. Despite this obstacle, we develop a quantum algorithm for dissipative quadratic n-dimensional ordinary differential equations. Assuming [Formula: see text], where R is a parameter characterizing the ratio of the nonlinearity and forcing to the linear dissipation, this algorithm has complexity [Formula: see text], where T is the evolution time, ϵ is the allowed error, and q measures decay of the solution. This is an exponential improvement over the best previous quantum algorithms, whose complexity is exponential in T. While exponential decay precludes efficiency, driven equations can avoid this issue despite the presence of dissipation. Our algorithm uses the method of Carleman linearization, for which we give a convergence theorem. This method maps a system of nonlinear differential equations to an infinite-dimensional system of linear differential equations, which we discretize, truncate, and solve using the forward Euler method and the quantum linear system algorithm. We also provide a lower bound on the worst-case complexity of quantum algorithms for general quadratic differential equations, showing that the problem is intractable for [Formula: see text] Finally, we discuss potential applications, showing that the [Formula: see text] condition can be satisfied in realistic epidemiological models and giving numerical evidence that the method may describe a model of fluid dynamics even for larger values of R.

9.
Genomics ; 115(5): 110666, 2023 09.
Artículo en Inglés | MEDLINE | ID: mdl-37315874

RESUMEN

Although high-throughput, cancer cell-line screening is a time-honored, important tool for anti-cancer drug development, this process involves the testing of each, individual drug in each, individual cell-line. Despite the availability of robotic liquid handling systems, this process remains a time-consuming and costly investment. The Broad Institute developed a new method called Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) to screen a mixture of barcoded, tumor cell-lines. Although this methodology significantly improved the efficiency of screening large numbers of cell-lines, the barcoding process itself was tedious that requires gene transfection and subsequent selection of stable cell-lines. In this study, we developed a new, genomic approach for screening multiple cancer cell-lines using endogenous "tags" that did not require prior barcoding: single nucleotide polymorphism-based, mixed-cell screening (SMICS). The code for SMICS is available at https://github.com/MarkeyBBSRF/SMICS.


Asunto(s)
Antineoplásicos , Polimorfismo de Nucleótido Simple , Línea Celular Tumoral , Genómica/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos
10.
Sensors (Basel) ; 24(16)2024 Aug 14.
Artículo en Inglés | MEDLINE | ID: mdl-39204946

RESUMEN

Foreign objects in coal flow easily cause damage to conveyor belts, and most foreign objects are often occluded, making them difficult to detect. Aiming at solving the problems of low accuracy and efficiency in the detection of occluded targets in a low-illumination and dust fog environment, an image detection method for foreign objects is proposed. Firstly, YOLOv5s back-end processing is optimized by soft non-maximum suppression to reduce the influence of dense objects. Secondly, SimOTA label allocation is used to reduce the influence of ambiguous samples under dense occlusion. Then, Slide Loss is used to excavate difficult samples, and Inner-SIoU is used to optimize the bounding box regression loss. Finally, Group-Taylor pruning is used to compress the model. The experimental results show that the proposed method has only 4.20 × 105 parameters, a computational amount of 1.00 × 109, a model size of 1.20 MB, and an mAP0.5 of up to 91.30% on the self-built dataset. The detection speed on the different computing devices is as high as 66.31, 41.90, and 33.03 FPS. This proves that the proposed method achieves fast and high-accuracy detection of multi-layer occluded coal flow foreign objects.

11.
Rev Cardiovasc Med ; 24(10): 298, 2023 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-39077565

RESUMEN

Background: Recommendations for drug treatment of left ventricular thrombus (LVT) are based on the ST-segment elevation myocardial infarction (STEMI) guidelines; however, the etiology of LVT has changed. Due to the lack of evidence regarding LVT treatment in the heart failure population, current heart failure guidelines do not cover LVT treatment. We sought to review the etiology of LVT and changes in antithrombotic therapy over the previous 12 years and explore the impact of anticoagulation treatment from a single center's experience. Methods: From January 2009 to June 2021, we studied 1675 patients with a discharge diagnosis of LVT at a single center to investigate the clinical characteristics, incidence of all-cause death, cardiovascular death, ischemic stroke, major adverse cardiac and cerebrovascular events (MACCE), systemic embolism (SE), and major bleeding events. Patients were divided into an anticoagulant group and a non-anticoagulant group according to whether they received oral anticoagulant therapy at discharge. Results: The study included 909 patients (anticoagulation, 510; no anticoagulation, 399). While overall antiplatelet therapy dramatically decreased, more patients with LVT received oral anticoagulation in 2021 (74.0%) than in 2009 (29.6%). In addition, more than half of the patients had heart failure with reduced ejection fraction (HFrEF) each year. The all-cause mortality was 17.3% during 3.8 years of follow-up. The incidences of cardiovascular death, stroke, MACCE, SE, and major bleeding were 16.0%, 3.3%, 19.8%, 5.1%, and 1.7%, respectively. The anticoagulation group had a significantly higher proportion of dilated cardiomyopathy than the non-anticoagulation group (24.7% vs. 5.5%, p < 0.001), and a lower LVEF (34.0 vs. 41.0, p < 0.001). The anticoagulation group also had a higher probability of adverse events on long-term follow-up (p > 0.05). A multivariable competing risk regression model found no significant difference in all six endpoints between the groups (all p > 0.05). Similar results were found by matched and weighted data analysis. Diabetes mellitus (hazard ratio (HR), 1.42; 95% confidence interval (CI), 1.04-1.93; p = 0.027), renal insufficiency (HR, 2.36; 95% CI, 1.60-3.50; p < 0.001), history of previous stroke (HR, 1.60; 95% CI, 1.13-2.29; p = 0.009), and HFrEF (HR, 2.54; 95% CI, 1.78-3.64; p < 0.001) were predictors of increased risk of MACCE. Conclusions: Heart failure, rather than acute myocardial infarction, is currently the primary cause of LVT. A trend towards better prognosis in the no anticoagulation group was noted. Multivariable, matching and weighting analysis showed no improvement in prognosis with anticoagulant therapy. Our study does not negate the efficacy of anticoagulation but suggests the need to strengthen the management of anticoagulation in order to achieve better efficacy.

12.
Opt Lett ; 48(15): 4077-4080, 2023 Aug 01.
Artículo en Inglés | MEDLINE | ID: mdl-37527122

RESUMEN

An iterative-based method for recovering the complex amplitude field behind scattering media is presented in this Letter. This method compensates the random phase modulation of scattering media by using multiple captured scattered light fields. Complex amplitude reconstruction with local iterative averaging of scattered light fields, and double weighted feedback is efficiently applied. Two feasible types of system setups, with varying detector positions and wavelength, are proposed. Simulations and proof-of-concept experiments are employed to demonstrate the effectiveness of the proposed method in reconstructing complex amplitude of a hidden target.

13.
Phys Rev Lett ; 131(15): 150603, 2023 Oct 13.
Artículo en Inglés | MEDLINE | ID: mdl-37897749

RESUMEN

We propose a simple method for simulating a general class of nonunitary dynamics as a linear combination of Hamiltonian simulation (LCHS) problems. LCHS does not rely on converting the problem into a dilated linear system problem or on the spectral mapping theorem. The latter is the mathematical foundation of many quantum algorithms for solving a wide variety of tasks involving nonunitary processes, such as the quantum singular value transformation. The LCHS method can achieve optimal cost in terms of state preparation. We also demonstrate an application for open quantum dynamics simulation using the complex absorbing potential method with near-optimal dependence on all parameters.

14.
Arch Biochem Biophys ; 743: 109663, 2023 07 15.
Artículo en Inglés | MEDLINE | ID: mdl-37290701

RESUMEN

OBJECTIVE: This study aimed to investigate the regulatory role of the PI3K/AKT/ERK signaling pathway in retinal fibrosis in -6.0 diopter (D) lens-induced myopic (LIM) guinea pigs. METHODS: Biological measurements of eye tissues were performed on guinea pigs to obtain their refraction, axial length, retinal thickness, physiological function, and fundus retinal status. In addition, Masson staining and immunohistochemical (IHC) assay were further done to explore the changes in retinal morphology after myopic induction. Meanwhile, hydroxyproline (HYP) content was measured to evaluate the degree of retinal fibrosis. Moreover, the levels of the PI3K/AKT/ERK signaling pathway and fibrosis-related molecules in retinal tissues including matrix metalloproteinase 2(MMP2), collagen type I (Collagen I), and α-smooth muscle actin (α-SMA) were detected by real-time quantitative PCR (qPCR) and Western blot. RESULTS: The LIM guinea pigs showed a significant myopic shift in refractive error and an increase in axial length compared with those of the normal control (NC) group. Masson staining, hydroxyproline content determination, and IHC showed an increase in retinal fibrosis. After myopic induction, qPCR and western blot analyses showed that phosphatidylinositol-3-kinase catalytic subunit α (PIK3CA), protein kinase B (AKT), extracellular regulated protein kinase 1/2 (ERK1/2), MMP2, Collagen I, and α-SMA were consistently elevated in the LIM group than those in the NC group. CONCLUSION: The PI3K/AKT/ERK signaling pathway was activated in the retinal tissues of myopic guinea pigs, which exaggerated fibrotic lesions and reduced retinal thickness, ultimately leading to retinal physiological dysfunctions in myopic guinea pigs.


Asunto(s)
Metaloproteinasa 2 de la Matriz , Miopía , Animales , Cobayas , Metaloproteinasa 2 de la Matriz/metabolismo , Proteínas Proto-Oncogénicas c-akt/metabolismo , Fosfatidilinositol 3-Quinasas/metabolismo , Hidroxiprolina , Miopía/metabolismo , Transducción de Señal , Fibrosis , Colágeno
15.
Bioinformatics ; 37(9): 1189-1197, 2021 06 09.
Artículo en Inglés | MEDLINE | ID: mdl-33165532

RESUMEN

MOTIVATION: Cancer somatic driver mutations associated with genes within a pathway often show a mutually exclusive pattern across a cohort of patients. This mutually exclusive mutational signal has been frequently used to distinguish driver from passenger mutations and to investigate relationships among driver mutations. Current methods for de novo discovery of mutually exclusive mutational patterns are limited because the heterogeneity in background mutation rate can confound mutational patterns, and the presence of highly mutated genes can lead to spurious patterns. In addition, most methods only focus on a limited number of pre-selected genes and are unable to perform genome-wide analysis due to computational inefficiency. RESULTS: We introduce a statistical framework, MEScan, for accurate and efficient mutual exclusivity analysis at the genomic scale. Our framework contains a fast and powerful statistical test for mutual exclusivity with adjustment of the background mutation rate and impact of highly mutated genes, and a multi-step procedure for genome-wide screening with the control of false discovery rate. We demonstrate that MEScan more accurately identifies mutually exclusive gene sets than existing methods and is at least two orders of magnitude faster than most methods. By applying MEScan to data from four different cancer types and pan-cancer, we have identified several biologically meaningful mutually exclusive gene sets. AVAILABILITY AND IMPLEMENTATION: MEScan is available as an R package at https://github.com/MarkeyBBSRF/MEScan. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Biología Computacional , Neoplasias , Algoritmos , Genómica , Humanos , Mutación , Neoplasias/genética
16.
Int J Mol Sci ; 23(12)2022 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-35742953

RESUMEN

Altered lipid metabolism is a potential target for therapeutic intervention in cancer. Overexpression of Fatty Acid Synthase (FASN) correlates with poor prognosis in colorectal cancer (CRC). While multiple studies show that upregulation of lipogenesis is critically important for CRC progression, the contribution of FASN to CRC initiation is poorly understood. We utilize a C57BL/6-Apc/Villin-Cre mouse model with knockout of FASN in intestinal epithelial cells to show that the heterozygous deletion of FASN increases mouse survival and decreases the number of intestinal adenomas. Using RNA-Seq and gene set enrichment analysis, we demonstrate that a decrease in FASN expression is associated with inhibition of pathways involved in cellular proliferation, energy production, and CRC progression. Metabolic and reverse phase protein array analyses demonstrate consistent changes in alteration of metabolic pathways involved in both anabolism and energy production. Downregulation of FASN expression reduces the levels of metabolites within glycolysis and tricarboxylic acid cycle with the most significant reduction in the level of citrate, a master metabolite, which enhances ATP production and fuels anabolic pathways. In summary, we demonstrate the critical importance of FASN during CRC initiation. These findings suggest that targeting FASN is a potential therapeutic approach for early stages of CRC or as a preventive strategy for this disease.


Asunto(s)
Adenoma , Neoplasias Colorrectales , Adenoma/genética , Animales , Línea Celular Tumoral , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/metabolismo , Modelos Animales de Enfermedad , Regulación hacia Abajo/genética , Acido Graso Sintasa Tipo I/genética , Acido Graso Sintasa Tipo I/metabolismo , Ácido Graso Sintasas/genética , Ácido Graso Sintasas/metabolismo , Ratones , Ratones Endogámicos C57BL , Transcriptoma
17.
Molecules ; 27(11)2022 May 26.
Artículo en Inglés | MEDLINE | ID: mdl-35684379

RESUMEN

A magnetic metal-organic framework nanocomposite (magnetic MIL-68(Ga)) was synthesized through a "one pot" reaction and used for heavy metal ion removal. The morphology and elemental properties of the nanocomposite were characterized by scanning electron microscopy (SEM), Fourier transform infrared (FT-IR), X-ray powder diffraction (XRD), as well as zeta potential. Moreover, the factors affecting the adsorption capacity of the nanocomposite, including time, pH, metal ion type and concentration, were studied. It was found that the adsorption capacity of magnetic MIL-68(Ga) for Pb2+ and Cu2+ was 220 and 130 mg/g, respectively. Notably, the magnetic adsorbents could be separated easily using an external magnetic field, regenerated by ethylenediaminetetraacetic acid disodium salt (EDTA-Na2) and reused three times, in favor of practical application. This study provides a reference for the rapid separation and purification of heavy metal ions from wastewater.


Asunto(s)
Estructuras Metalorgánicas , Metales Pesados , Contaminantes Químicos del Agua , Adsorción , Iones , Fenómenos Magnéticos , Estructuras Metalorgánicas/química , Espectroscopía Infrarroja por Transformada de Fourier , Contaminantes Químicos del Agua/química
18.
Molecules ; 27(20)2022 Oct 14.
Artículo en Inglés | MEDLINE | ID: mdl-36296473

RESUMEN

Soil enzymes, such as invertase, urease, acidic phosphatase and catalase, play critical roles in soil biochemical reactions and are involved in soil fertility. However, it remains a great challenge to efficiently concentrate soil enzymes and sensitively assess enzyme activity. In this study, we synthesized phenylboronic acid-functionalized magnetic nanoparticles to rapidly capture soil enzymes for sensitive soil enzyme assays. The iron oxide magnetic nanoparticles (MNPs) were firstly prepared by the co-precipitation method and then functionalized by (3-aminopropyl)triethoxysilane, polyethyleneimine and phenylboric acid in turn, obtaining the final nanoparticles (MNPPBA). Protein-capturing assays showed that the functionalized MNPs had a much higher protein-capturing capacity than the naked MNPs (56% versus 6%). Moreover, MNPPBA almost thoroughly captured the tested enzymes, i.e., urease, invertase, and alkaline phosphatase, from enzyme solutions. Based on MNPPBA, a soil enzyme assay method was developed by integration of enzyme capture, magnetic separation and trace enzyme analysis. The method was successfully applied in determining trace enzyme activity in rhizosphere soil. This study provides a strategy to sensitively determine soil enzyme activity for mechanistic investigation of soil fertility and plant-microbiome interaction.


Asunto(s)
Nanopartículas de Magnetita , Suelo , Catalasa , Ureasa , Polietileneimina , beta-Fructofuranosidasa , Fosfatasa Alcalina , Pruebas de Enzimas
19.
Clin Infect Dis ; 72(6): 1016-1023, 2021 03 15.
Artículo en Inglés | MEDLINE | ID: mdl-32100025

RESUMEN

BACKGROUND: Data on kidney transplantation (KTx) from hepatitis B surface antigen (HBsAg)-positive (HBsAg+) donors to HBsAg-negative (HBsAg-) recipients [D(HBsAg+)/R(HBsAg-)] are limited. We aimed to report the outcomes of D(HBsAg+)/R(HBsAg-) KTx in recipients with or without hepatitis B surface antibody (HBsAb). METHODS: Eighty-three D(HBsAg+)/R(HBsAg-) living KTx cases were retrospectively identified. The 384 cases of KTx from hepatitis B core antibody-positive (HBcAb+) living donors to HBcAb-negative (HBcAb-) recipients [D(HBcAb+)/R(HBcAb-)] were used as the control group. The primary endpoint was posttransplant HBsAg status change from negative to postive (-- →+). RESULTS: Before KTx, 24 donors (28.9%) in the D(HBsAg+)/R(HBsAg-) group were hepatitis B virus (HBV) DNA positive, and 20 recipients were HBsAb-. All 83 D(HBsAg+)/R(HBsAg-) recipients received HBV prophylaxis, while no D(HBcAb+)/R(HBcAb-) recipients received prophylaxis. After a median follow-up of 36 months (range, 6-106) and 36 months (range, 4-107) for the D(HBsAg+)/R(HBsAg-) and D(HBcAb+)/R(HBcAb-) groups, respectively, 2 of 83 (2.41%) D(HBsAg+)/R(HBsAg-) recipients and 1 of 384 (0.26%) D(HBcAb+)/R(HBcAb-) became HBsAg+, accompanied by HBV DNA-positive (P = .083). The 3 recipients with HBsAg-→+ were exclusively HBsAb-/HBcAb- before KTx. Recipient deaths were more frequent in the D(HBsAg+)/R(HBsAg-) group (6.02% vs 1.04%, P = .011), while liver and graft function, rejection, infection, and graft loss were not significantly different. In univariate analyses, pretransplant HBsAb-/HBcAb- combination in the D(HBsAg+)/R(HBsAg-) recipients carried a significantly higher risk of HBsAg-→+, HBV DNA-→+, and death. CONCLUSIONS: Living D(HBsAg+)/R(HBsAg-) KTx in HBsAb+ recipients provides excellent graft and patient survivals without HBV transmission. HBV transmission risks should be more balanced with respect to benefits of D(HBsAg+)/R(HBsAg-) KTx in HBsAb-/HBcAb- candidates.


Asunto(s)
Hepatitis B , Trasplante de Riñón , China/epidemiología , Hepatitis B/epidemiología , Anticuerpos contra la Hepatitis B , Antígenos de Superficie de la Hepatitis B , Virus de la Hepatitis B , Humanos , Donadores Vivos , Estudios Retrospectivos , Donantes de Tejidos
20.
Opt Lett ; 46(18): 4538-4541, 2021 Sep 15.
Artículo en Inglés | MEDLINE | ID: mdl-34525044

RESUMEN

Speckle correlation imaging (SCI) has found tremendous versatility compared with other scattering imaging approaches due to its single-shot data acquisition strategy, relatively simple optical setup, and high-fidelity reconstruction performance. However, this simplicity requires SCI experiments to be performed strictly in a darkroom condition. As background noise increases, the speckle contrast rapidly decreases, making precise interpretation of the data extremely difficult. Here, we demonstrate a method by refining the speckle in the autocorrelation domain to achieve high-performance single-shot imaging. Experiment results prove that our method is adapted to estimate objects in a low signal-to-background ratio (SBR) circumstance even if the SBR is about -23dB. Laboratory and outdoor SCI experiments are performed.

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