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1.
Sci Rep ; 11(1): 7991, 2021 04 12.
Artículo en Inglés | MEDLINE | ID: mdl-33846375

RESUMEN

To conquer the worldwide outbreak of COVID-19 virus, a large number of studies have been carried out on COVID-19 infection, transmission and treatment. However, few studies have been conducted from the perspectives of circRNA and lncRNA, which are known to be involved in regulating many life activities, such as immune tolerance and immune escapes, and hence may provide invaluable information in the emerging COVID-19 infection and recurrence. Moreover, exosomes has been reported to play an important role in COVID-19 recurrence, and thus may interact with the expression of circRNA and lncRNA. In this work, we sequenced circRNA, lncRNA and mRNA from recurrent COVID-19 patients and healthy people, and compared the differences. GO and KEGG enrichment analysis show that differentially expressed circRNA and lncRNA are mainly involved in the regulation of host cell cycle, apoptosis, immune inflammation, signaling pathway and other processes. The comparison to exosomes related databases shows that there are 114 differentially expressed circRNA, and 10 differentially expressed lncRNA related to exosomes. These studies provide reference for exploring circRNA and lncRNA to study the infection mechanism of COVID-19, their diagnostic and therapeutic values, as well as the possibility to employ them as biomarkers.


Asunto(s)
/sangre , ARN Circular/sangre , ARN Largo no Codificante/sangre , Apoptosis , Biomarcadores , Biología Computacional , Exosomas/metabolismo , Perfilación de la Expresión Génica , Regulación de la Expresión Génica , Humanos , Modelos Estadísticos , Análisis de Secuencia por Matrices de Oligonucleótidos , Reacción en Cadena de la Polimerasa , Recurrencia , Transducción de Señal
2.
BMC Bioinformatics ; 22(1): 193, 2021 Apr 15.
Artículo en Inglés | MEDLINE | ID: mdl-33858322

RESUMEN

BACKGROUND: ChIP-seq combines chromatin immunoprecipitation assays with sequencing and identifies genome-wide binding sites for DNA binding proteins. While many binding sites have strong ChIP-seq 'peak' observations and are well captured, there are still regions bound by proteins weakly, with a relatively low ChIP-seq signal enrichment. These weak binding sites, especially those at promoters and enhancers, are functionally important because they also regulate nearby gene expression. Yet, it remains a challenge to accurately identify weak binding sites in ChIP-seq data due to the ambiguity in differentiating these weak binding sites from the amplified background DNAs. RESULTS: ChIP-BIT2 ( http://sourceforge.net/projects/chipbitc/ ) is a software package for ChIP-seq peak detection. ChIP-BIT2 employs a mixture model integrating protein and control ChIP-seq data and predicts strong or weak protein binding sites at promoters, enhancers, or other genomic locations. For binding sites at gene promoters, ChIP-BIT2 simultaneously predicts their target genes. ChIP-BIT2 has been validated on benchmark regions and tested using large-scale ENCODE ChIP-seq data, demonstrating its high accuracy and wide applicability. CONCLUSION: ChIP-BIT2 is an efficient ChIP-seq peak caller. It provides a better lens to examine weak binding sites and can refine or extend the existing binding site collection, providing additional regulatory regions for decoding the mechanism of gene expression regulation.


Asunto(s)
Secuenciación de Nucleótidos de Alto Rendimiento , Programas Informáticos , Teorema de Bayes , Sitios de Unión , Inmunoprecipitación de Cromatina , Análisis de Secuencia por Matrices de Oligonucleótidos , Análisis de Secuencia de ADN
3.
BMC Bioinformatics ; 22(1): 188, 2021 Apr 13.
Artículo en Inglés | MEDLINE | ID: mdl-33849444

RESUMEN

BACKGROUND: The genomics data analysis has been widely used to study disease genes and drug targets. However, the existence of missing values in genomics datasets poses a significant problem, which severely hinders the use of genomics data. Current imputation methods based on a single learner often explores less known genomic data information for imputation and thus causes the imputation performance loss. RESULTS: In this study, multiple single imputation methods are combined into an imputation method by ensemble learning. In the ensemble method, the bootstrap sampling is applied for predictions of missing values by each component method, and these predictions are weighted and summed to produce the final prediction. The optimal weights are learned from known gene data in the sense of minimizing a cost function about the imputation error. And the expression of the optimal weights is derived in closed form. Additionally, the performance of the ensemble method is analytically investigated, in terms of the sum of squared regression errors. The proposed method is simulated on several typical genomic datasets and compared with the state-of-the-art imputation methods at different noise levels, sample sizes and data missing rates. Experimental results show that the proposed method achieves the improved imputation performance in terms of the imputation accuracy, robustness and generalization. CONCLUSION: The ensemble method possesses the superior imputation performance since it can make use of known data information more efficiently for missing data imputation by integrating diverse imputation methods and learning the integration weights in a data-driven way.


Asunto(s)
Algoritmos , Perfilación de la Expresión Génica , Expresión Génica , Análisis de Secuencia por Matrices de Oligonucleótidos , Tamaño de la Muestra
4.
Medicine (Baltimore) ; 100(16): e25433, 2021 Apr 23.
Artículo en Inglés | MEDLINE | ID: mdl-33879674

RESUMEN

ABSTRACT: Discoid lupus erythematosus (DLE) is the most common skin manifestation of lupus; however, the molecular mechanisms underlying DLE remain unknown. Therefore, we aimed to identify key differentially expressed genes (DEGs) in discoid lupus skin and investigate their potential pathways.To identify candidate genes involved in the occurrence and development of the disease, we downloaded the microarray datasets GSE52471 and GSE72535 from the Gene Expression Database (GEO). DEGs between discoid lupus skin and normal controls were selected using the GEO2R tool and Venn diagram software (http://bioinformatics.psb.ugent.be/webtools/Venn/). The Database for Annotation, Visualization, and Integrated Discovery (DAVID), Enrichr, and Cytoscape ClueGo were used to analyze the Kyoto Encyclopedia of Gene and Genome pathways and gene ontology. Protein-protein interactions (PPIs) of these DEGs were further assessed using the Search Tool for the Retrieval Interacting Genes version 10.0.Seventy three DEGs were co-expressed in both datasets. DEGs were predominantly upregulated in receptor signaling pathways of the immune response. In the PPI network, 69 upregulated genes were selected. Furthermore, 4 genes (CXCL10, ISG15, IFIH1, and IRF7) were found to be significantly upregulated in the RIG-I-like receptor signaling pathway, from analysis of Enrichr and Cytoscape ClueGo.The results of this study may provide new insights into the potential molecular mechanisms of DLE. However, further experimentation is required to confirm these findings.


Asunto(s)
Redes Reguladoras de Genes/inmunología , Lupus Eritematoso Discoide/genética , Quimiocina CXCL10/genética , Biología Computacional , Citocinas/genética , Proteína 58 DEAD Box/metabolismo , Conjuntos de Datos como Asunto , Perfilación de la Expresión Génica , Humanos , Factor 7 Regulador del Interferón/genética , Helicasa Inducida por Interferón IFIH1/genética , Lupus Eritematoso Discoide/epidemiología , Lupus Eritematoso Discoide/inmunología , Lupus Eritematoso Discoide/patología , Análisis de Secuencia por Matrices de Oligonucleótidos , Mapeo de Interacción de Proteínas , Mapas de Interacción de Proteínas/genética , Mapas de Interacción de Proteínas/inmunología , Receptores Inmunológicos/metabolismo , Transducción de Señal/genética , Transducción de Señal/inmunología , Piel/inmunología , Piel/patología , Programas Informáticos , Ubiquitinas/genética , Regulación hacia Arriba/inmunología
5.
Biol Res ; 54(1): 12, 2021 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-33795012

RESUMEN

BACKGROUND: Multiple sclerosis (MS) is a central nervous system disease with a high disability rate. Modern molecular biology techniques have identified a number of key genes and diagnostic markers to MS, but the etiology and pathogenesis of MS remain unknown. RESULTS: In this study, the integration of three peripheral blood mononuclear cell (PBMC) microarray datasets and one peripheral blood T cells microarray dataset allowed comprehensive network and pathway analyses of the biological functions of MS-related genes. Differential expression analysis identified 78 significantly aberrantly expressed genes in MS, and further functional enrichment analysis showed that these genes were associated with innate immune response-activating signal transduction (p = 0.0017), neutrophil mediated immunity (p = 0.002), positive regulation of innate immune response (p = 0.004), IL-17 signaling pathway (p < 0.035) and other immune-related signaling pathways. In addition, a network of MS-specific protein-protein interactions (PPI) was constructed based on differential genes. Subsequent analysis of network topology properties identified the up-regulated CXCR4, ITGAM, ACTB, RHOA, RPS27A, UBA52, and RPL8 genes as the hub genes of the network, and they were also potential biomarkers of MS through Rap1 signaling pathway or leukocyte transendothelial migration. RT-qPCR results demonstrated that CXCR4 was obviously up-regulated, while ACTB, RHOA, and ITGAM were down-regulated in MS patient PBMC in comparison with normal samples. Finally, support vector machine was employed to establish a diagnostic model of MS with a high prediction performance in internal and external datasets (mean AUC = 0.97) and in different chip platform datasets (AUC = (0.93). CONCLUSION: This study provides new understanding for the etiology/pathogenesis of MS, facilitating an early identification and prediction of MS.


Asunto(s)
Biomarcadores , Perfilación de la Expresión Génica , Leucocitos Mononucleares , Esclerosis Múltiple , Biología Computacional , Redes Reguladoras de Genes , Humanos , Esclerosis Múltiple/diagnóstico , Esclerosis Múltiple/genética , Análisis de Secuencia por Matrices de Oligonucleótidos
6.
BMC Cancer ; 21(1): 233, 2021 Mar 06.
Artículo en Inglés | MEDLINE | ID: mdl-33676448

RESUMEN

BACKGROUND: It was demonstrated that multifunctional protein APE1 (Apurinic/apyrimidinic endonuclease 1) is closely related to tumor immune microenvironment in a number of investigations, Meanwhile, the abundance of tumor infiltrating lymphocytes (TILs) has been shown as a prognosis indicator in some researches. However, it remains unclear whether APE1 is involved in the process of TILs affecting the prognosis of patients. To this end, we investigated the associations between APE1 and TILs in non-small cell lung cancer (NSCLC) and explored whether APE1 would influence the associations of CD4+ T cells infiltration with the prognosis of patients. METHODS: Genome-wide expression datasets were obtained from the Gene Expression Omnibus (GEO) public database under accession number GSE68465, GSE30219, GSE31210 and GSE50081. MCPcounter and CIBERSORT analysis was conducted to evaluate the abundance of TILs in 1006 NSCLC patients of GEO database. Spearman correlation tests were used to evaluate correlations between abundance of various TILs and APE1 expression. RFS (recurrence free survival) was estimated using the Kaplan-Meier method and the Cox proportional-hazards model. The expression level of APE1 and tumor-infiltrating CD4+ T cells was evaluated by immunohistochemistry (IHC). RESULTS: The results showed that the abundance of CD4+ naïve T cells was negatively associated with the APE1 expression. CD4+ naïve T cells infiltration was a favorable prognostic factor for RFS, however, there was no effect of CD4+ T cells infiltration on RFS in patients with high APE1 expression. Subsequently, it was further confirmed that CD4+ T cells infiltration was negatively associated with the APE1 expression level in 108 NSCLC tissue samples; high CD4+ T cells infiltration was associated with longer RFS in low APE1 expression group but not in APE1 high expression group. CONCLUSION: These results suggested that APE1 may affect the relationship between CD4+ T cells infiltration and prognosis in NSCLC. This study provides new insights into predictors of outcome in patients with NSCLC, and suggests that combining immunotherapy and APE1-targeted therapy may be a promising treatment for NSCLC.


Asunto(s)
Carcinoma de Pulmón de Células no Pequeñas/mortalidad , ADN-(Sitio Apurínico o Apirimidínico) Liasa/metabolismo , Neoplasias Pulmonares/mortalidad , Recurrencia Local de Neoplasia/epidemiología , Antineoplásicos Inmunológicos/farmacología , Antineoplásicos Inmunológicos/uso terapéutico , Protocolos de Quimioterapia Combinada Antineoplásica/farmacología , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapéutico , Linfocitos T CD4-Positivos/efectos de los fármacos , Linfocitos T CD4-Positivos/inmunología , Carcinoma de Pulmón de Células no Pequeñas/inmunología , Carcinoma de Pulmón de Células no Pequeñas/patología , Carcinoma de Pulmón de Células no Pequeñas/terapia , Quimioterapia Adyuvante/métodos , ADN-(Sitio Apurínico o Apirimidínico) Liasa/antagonistas & inhibidores , Conjuntos de Datos como Asunto , Supervivencia sin Enfermedad , Femenino , Perfilación de la Expresión Génica , Humanos , Estimación de Kaplan-Meier , Pulmón/inmunología , Pulmón/patología , Pulmón/cirugía , Neoplasias Pulmonares/inmunología , Neoplasias Pulmonares/patología , Neoplasias Pulmonares/terapia , Linfocitos Infiltrantes de Tumor/efectos de los fármacos , Linfocitos Infiltrantes de Tumor/inmunología , Masculino , Persona de Mediana Edad , Recurrencia Local de Neoplasia/inmunología , Recurrencia Local de Neoplasia/prevención & control , Análisis de Secuencia por Matrices de Oligonucleótidos , Neumonectomía , Pronóstico , Microambiente Tumoral/efectos de los fármacos , Microambiente Tumoral/inmunología
7.
BMC Cancer ; 21(1): 277, 2021 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-33722210

RESUMEN

BACKGROUND: As one of the novel molecules, circRNA has been identified closely involved in the pathogenesis of many diseases. However, the function of circRNA in acute myeloid leukemia (AML) still remains unknown. METHODS: In the current study, the RNA expression profiles were obtained from Gene Expression Omnibus (GEO) datasets. The differentially expressed RNAs were identified using R software and the competing endogenous RNA (ceRNA) network was constructed using Cytoscape. Functional and pathway enrichment analyses were performed to identify the candidate circRNA-mediated aberrant signaling pathways. The hub genes were identified by MCODE and CytoHubba plugins of Cytoscape, and then a subnetwork regulatory module was established. RESULTS: A total of 27 circRNA-miRNA pairs and 208 miRNA-mRNA pairs, including 12 circRNAs, 24 miRNAs and 112 mRNAs were included in the ceRNA network. Subsequently, a subnetwork, including 4 circRNAs, 5 miRNAs and 6 mRNAs, was established based on related circRNA-miRNA-mRNA regulatory modules. CONCLUSIONS: In summary, this work analyzes the characteristics of circRNA as competing endogenous RNA in AML pathogenesis, which would provide hints for developing novel prognostic, diagnostic and therapeutic strategy for AML.


Asunto(s)
Biomarcadores de Tumor/metabolismo , Regulación Neoplásica de la Expresión Génica , Redes Reguladoras de Genes , Leucemia Mieloide Aguda/genética , ARN Circular/metabolismo , Biomarcadores de Tumor/análisis , Biología Computacional , Conjuntos de Datos como Asunto , Perfilación de la Expresión Génica , Humanos , Leucemia Mieloide Aguda/diagnóstico , Leucemia Mieloide Aguda/mortalidad , MicroARNs/metabolismo , Análisis de Secuencia por Matrices de Oligonucleótidos , Pronóstico , Mapeo de Interacción de Proteínas , Mapas de Interacción de Proteínas/genética , ARN Circular/análisis , ARN Mensajero/metabolismo , Transducción de Señal/genética , Análisis de Supervivencia
8.
Sensors (Basel) ; 21(4)2021 Feb 16.
Artículo en Inglés | MEDLINE | ID: mdl-33669434

RESUMEN

Microfabrication and Polydimethylsiloxane (PDMS) soft-lithography techniques became popular for microfluidic prototyping at the lab, but even after protocol optimization, fabrication is yet a long, laborious process and partly user-dependent. Furthermore, the time and money required for the master fabrication process, necessary at any design upgrade, is still elevated. Digital Manufacturing (DM) and Rapid-Prototyping (RP) for microfluidics applications arise as a solution to this and other limitations of photo and soft-lithography fabrication techniques. Particularly for this paper, we will focus on the use of subtractive DM techniques for Organ-on-a-Chip (OoC) applications. Main available thermoplastics for microfluidics are suggested as material choices for device fabrication. The aim of this review is to explore DM and RP technologies for fabrication of an OoC with an embedded membrane after the evaluation of the main limitations of PDMS soft-lithography strategy. Different material options are also reviewed, as well as various bonding strategies. Finally, a new functional OoC device is showed, defining protocols for its fabrication in Cyclic Olefin Polymer (COP) using two different RP technologies. Different cells are seeded in both sides of the membrane as a proof of concept to test the optical and fluidic properties of the device.


Asunto(s)
Dispositivos Laboratorio en un Chip , Microfluídica , Microtecnología , Análisis de Secuencia por Matrices de Oligonucleótidos , Polímeros
9.
Sensors (Basel) ; 21(4)2021 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-33671996

RESUMEN

Organ-on-chip devices have provided the pharmaceutical and tissue engineering worlds much hope since they arrived and began to grow in sophistication. However, limitations for their applicability were soon realized as they lacked real-time monitoring and sensing capabilities. The users of these devices relied solely on endpoint analysis for the results of their tests, which created a chasm in the understanding of life between the lab the natural world. However, this gap is being bridged with sensors that are integrated into organ-on-chip devices. This review goes in-depth on different sensing methods, giving examples for various research on mechanical, electrical resistance, and bead-based sensors, and the prospects of each. Furthermore, the review covers works conducted that use specific sensors for oxygen, and various metabolites to characterize cellular behavior and response in real-time. Together, the outline of these works gives a thorough analysis of the design methodology and sophistication of the current sensor integrated organ-on-chips.


Asunto(s)
Dispositivos Laboratorio en un Chip , Impedancia Eléctrica , Análisis de Secuencia por Matrices de Oligonucleótidos
10.
Gene ; 785: 145605, 2021 Jun 15.
Artículo en Inglés | MEDLINE | ID: mdl-33771603

RESUMEN

OBJECTIVE: Parentage analysis is a technology that uses genetic methods to verify or exclude relationships between individuals. STR technology is often used in parentage analysis. We received three sets of samples from three families. Each set of samples consisted of a male individual and a female individual. Their test requirements were meant to determine whether they were a paternity relationship, a sibling relationship, or grandparent-grandchild relationship. However, only one STR locus mismatch was detected in each group. Other family members to assist in testing could not be identified; therefore, other methods were needed to assist in judgment. Using high-density SNP microarrays, we analyzed the feasibility of its application in paternity analysis. RESULTS: A total of 180 samples were tested, including 100 unrelated samples, and 74 samples from 30 families, and six samples from three families. The data were analyzed, grouped according to the chromosome of SNP, and the mismatching rate was counted. The total mismatching rate of SNP in unrelated individuals was 8-10 times higher than that of parent-child individuals. Individuals with a total mismatch rate of more than 5.3% were defined as individuals with no kinship, and the individuals with a total mismatch rate of less than 0.6% were defined as the individuals with a parent-child relationship. CONCLUSIONS: Through the use of high-density gene chips for analysis, we also completed an auxiliary analysis of the kinship of the three families. The gene chip is a better method for auxiliary analysis of the kinship between individuals.


Asunto(s)
Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Linaje , Polimorfismo de Nucleótido Simple , Adulto , Niño , Estudios de Factibilidad , Femenino , Técnicas de Genotipaje , Humanos , Masculino , Repeticiones de Microsatélite , Paternidad
11.
Methods Mol Biol ; 2212: 245-264, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33733360

RESUMEN

The changes in gene expression under microarray technology are valuable to recognize and study the evolution process of species or diseases. Among the existing methods of analyzing the changes in gene expression, statistical method is one of the common and accurate approaches. This paper presents a step-by-step protocol to use Biopeak, a statistical tool to identify and visualize any significant impulse-like change of the gene expression in genomic series data. Biopeak focuses on the temporal features of the gene expression as signals. Through the statistical approaches including finding the local maximum and subsequent filtering, the potential changes are detected as the peak of signals. To filter the outliers and mark the significant changes, the correlation heatmap and clustering approach can be applied. Biopeak also provides several clustering techniques with different cluster abilities for result comparison. The step-by-step application of Biopeak is carried out by running the dataset of human epithelial cells in response to heat. The results of the peak detection, the correlation heatmap, and the clustering are demonstrated.


Asunto(s)
Algoritmos , Análisis por Conglomerados , Biología Computacional/métodos , Epistasis Genética , Células Epiteliales/metabolismo , Células Cultivadas , Células Epiteliales/citología , Perfilación de la Expresión Génica , Calor , Humanos , Análisis de Secuencia por Matrices de Oligonucleótidos , Análisis de la Célula Individual , Programas Informáticos
12.
Methods Mol Biol ; 2212: 377-400, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33733368

RESUMEN

Complex genetic interactions occur when mutant alleles of multiple genes combine to elicit an unexpected phenotype, which could not be predicted given the expectation based on the combination of phenotypes associated with individual mutant alleles. Trigenic Synthetic Genetic Array (τ-SGA) methodology was developed for the systematic analysis of complex interactions involving combinations of three gene perturbations. With a series of replica pinning steps of the τ-SGA procedure, haploid triple mutants are constructed through automated mating and meiotic recombination. For example, a double-mutant query strain carrying two mutant alleles of interest, such as a deletion allele of a nonessential gene and a conditional temperature-sensitive allele of an essential gene, is crossed to an input array of yeast mutants, such as the diagnostic array set of ~1200 mutants, to generate an output array of triple mutants. The colony-size measurements of the resulting triple mutants are used to estimate cellular fitness and quantify trigenic interactions by incorporating corresponding single- and double-mutant fitness estimates. Trigenic interaction networks can be further analyzed for functional modules using various clustering and enrichment analysis tools. Complex genetic interactions are rich in functional information and provide insight into the genotype-to-phenotype relationship, genome size, and speciation.


Asunto(s)
Epistasis Genética , Regulación Fúngica de la Expresión Génica , Redes Reguladoras de Genes , Genes Fúngicos , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Saccharomyces cerevisiae/genética , Alelos , Genes Esenciales , Genes Sintéticos , Genotipo , Haploidia , Mutación , Fenotipo , Saccharomyces cerevisiae/metabolismo
14.
Zhonghua Yi Xue Za Zhi ; 101(8): 573-578, 2021 Mar 02.
Artículo en Chino | MEDLINE | ID: mdl-33663188

RESUMEN

Objective: To explore the difference in the expression profile of circular RNA in peripheral blood mononuclear cells between patients with mild and severe influenza pneumonia. Methods: From December 2018 to March 2019, 10 inpatients with mild and 10 inpatients with severe influenza pneumonia admitted to the Department of Infection and Clinical Microbiology of Beijing Chaoyang Hospital were included. Clariom™ D gene chip was used to explore the circRNA expression profiles of peripheral blood mononuclear cells (PBMC) isolated from the patients. The absolute value of the fold change (FC value)>2 and P<0.05 were used as the criteria to screen the differentially expressed circRNA, and the gene ontology (GO) enrichment analysis and the Kyoto Encyclopedia of Gene and Genome database (Kyoto Encyclopedia of Genes and Genomes, KEGG) signal pathway enrichment analysis were also performed. Results: The age of mild patients [M (P25, P75)] was 62.0 (34.5, 69.8) years old, including 4 males; the age of severe patients [M (P25, P75)] was 50.0 (37.0, 60.0) years old, all were males. A total of 137 differentially expressed circRNAs in PBMCs of mild and severe patients were screened. The numbers of up-regulated and down-regulated circRNAs in mild patients were 101 and 36, respectively. Among them, hsa_circ_0091073 (FC value=160.898, P<0.05) was the most significantly up-regulated circRNA and hsa_circ_0092219 (FC value =-17.630, P<0.05) was the most significantly down-regulated circRNA. GO enrichment analysis showed that a total of 111 secondary GO items were significantly associated with related differential expression of circRNA (P<0.05). The GO terms associated with upregulated circRNAs included DNA-templated transcription, regulation of DNA-templated transcription, regulation of transcription from RNA polymerase Ⅱ promoter, etc.; The GO terms associated with downregulated circRNAs included neutrophil degranulation, killing of cells of other organism, defense response to fungus, etc. KEGG signaling pathway analysis showed that there were 37 metabolic pathways related to differentially expressed circRNAs (P<0.05). Signaling pathways related to up-regulated circRNAs included nuclear factor-κB (NF-κB) signaling pathway, mitogen-activated protein kinase (MAPK) signaling pathway, tumor necrosis factor (TNF) signaling pathway, etc. Signaling pathways related to down-regulation of circRNAs included cancer transcription disorders, folate carbon pool, and other types of O-glycan biosynthesis. Conclusion: The expression of circRNA in PBMC of mild and severe influenza pneumonia patients is significantly different, and it may play a role in the pathogenic mechanism of influenza pneumonia through multiple signal pathways.


Asunto(s)
Gripe Humana , Neumonía , Anciano , Humanos , Gripe Humana/genética , Leucocitos Mononucleares , Masculino , Persona de Mediana Edad , Análisis de Secuencia por Matrices de Oligonucleótidos , ARN Circular
15.
Methods Mol Biol ; 2269: 205-219, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33687681

RESUMEN

Gene Expression Music Algorithms (GEMusicA) use the transformation of gene expression data into melodies for the representation of sample-specific gene expression patterns. Quantitative analysis of similarities between melodies can be used for sample classification. The same algorithm can be used as simple and efficient encryption method. Here, we describe the usage of GEMusicA for the analyses of gene expression data from different stem cell types and stem cell-like tumor cells.


Asunto(s)
Algoritmos , Diferenciación Celular , Regulación de la Expresión Génica , Análisis de Secuencia por Matrices de Oligonucleótidos , Células Madre/metabolismo , Humanos
16.
Nat Commun ; 12(1): 1395, 2021 03 02.
Artículo en Inglés | MEDLINE | ID: mdl-33654088

RESUMEN

On-chip glycan biosynthesis is an effective strategy for preparing useful complex glycan sources and for preparing glycan-involved applications simultaneously. However, current methods have some limitations when analyzing biosynthesized glycans and optimizing enzymatic reactions, which could result in undefined glycan structures on a surface, leading to unequal and unreliable results. In this work, a glycan chip is developed by introducing a pH-responsive i-motif DNA linker to control the immobilization and isolation of glycans on chip surfaces in a pH-dependent manner. On-chip enzymatic glycosylations are optimized for uniform biosynthesis of cancer-associated Globo H hexasaccharide and its related complex glycans through stepwise quantitative analyses of isolated products from the surface. Successful interaction analyses of the anti-Globo H antibody and MCF-7 breast cancer cells with on-chip biosynthesized Globo H-related glycans demonstrate the feasibility of the structure-switchable DNA linker-based glycan chip platform for on-chip complex glycan biosynthesis and glycan-involved applications.


Asunto(s)
ADN/metabolismo , Neoplasias/metabolismo , Polisacáridos/biosíntesis , Antígenos de Carbohidratos Asociados a Tumores/metabolismo , Toxina del Cólera/metabolismo , Gangliósido G(M1)/metabolismo , Glicosilación , Humanos , Concentración de Iones de Hidrógeno , Células MCF-7 , Análisis de Secuencia por Matrices de Oligonucleótidos , Polisacáridos/química , Subunidades de Proteína/metabolismo
17.
Medicine (Baltimore) ; 100(6): e24471, 2021 Feb 12.
Artículo en Inglés | MEDLINE | ID: mdl-33578541

RESUMEN

BACKGROUND: In osteosarcoma, the lung is the most common metastatic organ. Intensive work has been made to illuminate the pathogeny, but the specific metastatic mechanism remains unclear. Thus, we conducted the study to seek to find the key genes and critical functional pathways associated with progression and treatment in lung metastasis originating from osteosarcoma. METHODS: Two independent datasets (GSE14359 and GSE85537) were screened out from the Gene Expression Omnibus (GEO) database and the overlapping differentially expressed genes (DEGs) were identified using GEO2R online platform. Subsequently, the Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analysis of DEGs were conducted using DAVID. Meanwhile, the protein-protein interaction (PPI) network constructed by STRING was visualized using Cytoscape. Afterwards, the key module and hub genes were extracted from the PPI network using the MCODE and cytoHubba plugin. Moreover, the raw data obtained from GSE73166 and GSE21257 were applied to verify the expression differences and conduct the survival analyses of hub genes, respectively. Finally, the interaction network of miRNAs and hub genes constructed by ENCORI was visualized using Cytoscape. RESULTS: A total of 364 DEGs were identified, comprising 96 downregulated genes and 268 upregulated genes, which were mainly involved in cancer-associated pathways, adherens junction, ECM-receptor interaction, focal adhesion, MAPK signaling pathway. Subsequently, 10 hub genes were obtained and survival analysis demonstrated SKP2 and ASPM were closely related to poor prognosis of patients with osteosarcoma. Finally, hsa-miR-340-5p, has-miR-495-3p, and hsa-miR-96-5p were found to be most closely associated with these hub genes according to the interaction network of miRNAs and hub genes. CONCLUSION: The key genes and functional pathways identified in the study may contribute to understanding the molecular mechanisms involved in the carcinogenesis and progression of lung metastasis originating from osteosarcoma, and provide potential diagnostic and therapeutic targets.


Asunto(s)
Neoplasias Óseas/patología , Neoplasias Pulmonares/secundario , Osteosarcoma/patología , Neoplasias Óseas/diagnóstico , Neoplasias Óseas/genética , Biología Computacional , Regulación Neoplásica de la Expresión Génica/genética , Redes Reguladoras de Genes/genética , Genes Relacionados con las Neoplasias/genética , Marcadores Genéticos , Humanos , Neoplasias Pulmonares/diagnóstico , Neoplasias Pulmonares/genética , MicroARNs/genética , Análisis de Secuencia por Matrices de Oligonucleótidos , Osteosarcoma/diagnóstico , Osteosarcoma/genética , Transducción de Señal/genética
18.
Life Sci ; 275: 119273, 2021 Jun 15.
Artículo en Inglés | MEDLINE | ID: mdl-33631172

RESUMEN

AIMS: Postmenopausal osteoporosis (PMOP) is a growing health problem affecting many postmenopausal women. This study intended to identify the role of dexmedetomidine (Dex) in osteoporosis (OP). MAIN METHODS: Microarray analysis was performed for the gene expression profiles of PMOP patients and postmenopausal healthy volunteers, and the most differentially expressed microRNA (miR)-361-5p was verified in clinic, and its diagnostic value in PMOP patients was analyzed. After establishment of OP model by ovariectomy, Dex treatment and overexpression of miR-361-5p or vascular endothelial growth factor A (VEGFA) were performed in OP rats or isolated bone marrow mesenchymal stem cells (BMSCs). Bone mineral density (BMD) related indexes and levels of osteogenesis-angiogenesis related genes were measured. The apoptosis and osteogenic differentiation of BMSCs were detected. After human umbilical vein endothelial cells (HUVECs) and BMSCs were cocultured, the angiogenesis of BMSCs was detected by Matrigel-based angiogenesis experiment. KEY FINDINGS: miR-361-5p was highly expressed in PMOP patients and OP rats, with good diagnostic effect on PMOP. After Dex treatment, the expressions of miR-361-5p, VEGFA, BMD related indexes were increased in OP rats. In BMSCs, level of osteogenesis-angiogenesis related genes were increased after adding Dex, and the apoptosis was decreased after coculture of HUVECs and BMSCs. miR-361-5p could target VEGFA. After miR-361-5p overexpression + Dex treatment, the indexes related to osteogenesis and angiogenesis in OP rats and BMSCs were decreased, which were reversed after further overexpressing VEGFA. SIGNIFICANCE: Dex can enhance VEGFA by inhibiting miR-361-5p, and then promote osteogenesis-angiogenesis, thus providing potential targets for PMOP treatment.


Asunto(s)
Dexmedetomidina/farmacología , MicroARNs/metabolismo , Neovascularización Fisiológica/efectos de los fármacos , Osteogénesis/efectos de los fármacos , Osteoporosis Posmenopáusica/tratamiento farmacológico , Factor A de Crecimiento Endotelial Vascular/metabolismo , Anciano , Animales , Densidad Ósea , Dexmedetomidina/uso terapéutico , Femenino , Citometría de Flujo , Humanos , MicroARNs/fisiología , Persona de Mediana Edad , Análisis de Secuencia por Matrices de Oligonucleótidos , Osteoporosis Posmenopáusica/fisiopatología , Ratas , Ratas Sprague-Dawley , Reacción en Cadena en Tiempo Real de la Polimerasa , Factor A de Crecimiento Endotelial Vascular/fisiología
19.
BMC Infect Dis ; 21(1): 230, 2021 Feb 27.
Artículo en Inglés | MEDLINE | ID: mdl-33639884

RESUMEN

BACKGROUND: Respiratory tract infections (RTIs) are the common diseases in children and the routine detection methods frequently fail to identify the infectious pathogens especially for viruses. The Filmarray respiratory panel (FARP) can reliably and rapidly identify viruses and bacteria pathogens. This study is to evaluate the performance and clinical significance of FARP in children. METHODS: Children diagnosed with RTIs in pediatric intensive care unit (PICU) were enrolled in this study. Nasopharyngeal secretion (NPS) samples of these children were collected and the FARP assay for 17 pathogens and routine microbiological methods were performed. Clinical data of all patients was also collected and evaluated. RESULTS: A total of 90 children were enrolled into this study and 58 patients (64.4%) were positive for 13 pathogens by FARP, with 18 being detected positive with multiple-virus (31.3%, 18/58). Human rhinovirus/enterovirus (21.0%%, 17/58) were the predominant pathogen, followed by adenovirus (18.5%). Higher proportions of various pathogens were identified in the infant and toddler (0-2 years) groups with human rhinovirus/enterovirus being mostly virus. Adenovirus were common in the group aged 3-5 years, but only three pathogens including M.pneumoniae, respiratory syncytial virus, and adenovirus were also found in age group (6-14 years). Among 58 FARP positive patients, significant differences were found in antibiotic prescription and use of glucocorticoid between the single-organism-positive group and the multi-organism-positive group (P < 0.05). Furthermore, there was significant difference in use of anti-virus and usage of glucocorticoid between severe respiratory infections group and non severe respiratory infections group (P < 0.05). CONCLUSIONS: This study demonstrated that FARP can provide the rapid detection of respiratory virus and atypical bacteria for children, especially with severe respiratory tract infections.


Asunto(s)
Técnicas Microbiológicas/métodos , Reacción en Cadena de la Polimerasa Multiplex/métodos , Infecciones del Sistema Respiratorio/diagnóstico , Virología/métodos , Adolescente , Edad de Inicio , Bacterias/genética , Bacterias/aislamiento & purificación , Niño , Preescolar , Diagnóstico Diferencial , Femenino , Humanos , Lactante , Recién Nacido , Unidades de Cuidado Intensivo Pediátrico , Masculino , Nasofaringe/microbiología , Nasofaringe/virología , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Valor Predictivo de las Pruebas , Reproducibilidad de los Resultados , Infecciones del Sistema Respiratorio/epidemiología , Infecciones del Sistema Respiratorio/microbiología , Infecciones del Sistema Respiratorio/virología , Estudios Retrospectivos , Virus/genética , Virus/aislamiento & purificación
20.
Gene ; 782: 145537, 2021 May 25.
Artículo en Inglés | MEDLINE | ID: mdl-33636294

RESUMEN

Detection of TCGA data revealed that WIPI1 is highly expressed in osteosarcoma cells. So we explore the mechanisms of WIPI1 affecting the proliferation of osteosarcoma cells through Affymetrix microarray analysis. Functional analysis of differentially expressed genes shows that the classical signaling pathways affecting tumor formation and development have changed significantly. By fitting analysis, it is speculated that the WIPI1 may function in the direction of osteosarcoma by regulating the expression of multiple cell cycle-related genes such as CDKN1A, CDK4 and CCND1. Therefore, the key genes are selected for RT-PCR and Western-blot verification. Combined with flow and other means, WIPI1 may affect the cell cycle and the osteosarcoma by regulating the expression of CDKN1A, CDK4 and CCND1. To verify the results, the effect of WIPI1 on cell proliferation was quantified by MTT, cell counts and nude mouse tumorigenicity assay. The results showed that WIPI1 promotes osteosarcoma cell proliferation.


Asunto(s)
Proteínas Relacionadas con la Autofagia/genética , Neoplasias Óseas/genética , Proliferación Celular/genética , Inhibidor p21 de las Quinasas Dependientes de la Ciclina/antagonistas & inhibidores , Proteínas de la Membrana/genética , Osteosarcoma/genética , Animales , Proteínas Relacionadas con la Autofagia/fisiología , Neoplasias Óseas/patología , Ciclo Celular/genética , Inhibidor p21 de las Quinasas Dependientes de la Ciclina/genética , Regulación Neoplásica de la Expresión Génica , Vectores Genéticos , Células HEK293 , Humanos , Lentivirus/genética , Proteínas de la Membrana/fisiología , Ratones Desnudos , Análisis de Secuencia por Matrices de Oligonucleótidos , Osteosarcoma/patología , Programas Informáticos , Transcriptoma
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