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1.
Mol Genet Genomics ; 295(1): 209-219, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31642957

RESUMEN

The objective of this study was to map the quantitative trait loci (QTLs) for chip color after harvest (AH), cold storage (CS) and after reconditioning (RC) in diploid potato and compare them with QTLs for starch-corrected chip color. Chip color traits AH, CS, and RC significantly correlated with tuber starch content (TSC). To limit the effect of starch content, the chip color was corrected for TSC. The QTLs for chip color (AH, CS, and RC) and the starch-corrected chip color determined with the starch content after harvest (SCAH), after cold storage (SCCS) and after reconditioning (SCRC) were compared to assess the extent of the effect of starch and the location of genetic factors underlying this effect on chip color. We detected QTLs for the AH, CS, RC and starch-corrected traits on ten potato chromosomes, confirming the polygenic nature of the traits. The QTLs with the strongest effects were detected on chromosomes I (AH, 0 cM, 11.5% of variance explained), IV (CS, 43.9 cM, 12.7%) and I (RC, 49.7 cM, 14.1%). When starch correction was applied, the QTLs with the strongest effects were revealed on chromosomes VIII (SCAH, 39.3 cM, 10.8% of variance explained), XI (SCCS, 79.5 cM, 10.9%) and IV (SCRC, 43.9 cM, 10.8%). Applying the starch correction changed the landscape of QTLs for chip color, as some QTLs became statistically insignificant, shifted or were refined, and new QTLs were detected for SCAH. The QTLs on chromosomes I and IV were significant for all traits with and without starch correction.


Asunto(s)
Sitios de Carácter Cuantitativo/genética , Solanum tuberosum/genética , Almidón/genética , Mapeo Cromosómico/métodos , Color , Diploidia , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Tubérculos de la Planta/genética
2.
Gene ; 726: 144168, 2020 Feb 05.
Artículo en Inglés | MEDLINE | ID: mdl-31759986

RESUMEN

Methods based around statistics and linear algebra have been increasingly used in attempts to address emerging questions in microarray literature. Microarray technology is a long-used tool in the global analysis of gene expression, allowing for the simultaneous investigation of hundreds or thousands of genes in a sample. It is characterized by a low sample size and a large feature number created a non-square matrix, and by the incomplete rank, that can generate countless more solution in classifiers. To avoid the problem of the 'curse of dimensionality' many authors have performed feature selection or reduced the size of data matrix. In this work, we introduce a new logistic regression-based model to classify breast cancer tumor samples based on microarray expression data, including all features of gene expression and without reducing the microarray data matrix. If the user still deems it necessary to perform feature reduction, it can be done after the application of the methodology, still maintaining a good classification. This methodology allowed the correct classification of breast cancer sample data sets from Gene Expression Omnibus (GEO) data series GSE65194, GSE20711, and GSE25055, which contain the microarray data of said breast cancer samples. Classification had a minimum performance of 80% (sensitivity and specificity), and explored all possible data combinations, including breast cancer subtypes. This methodology highlighted genes not yet studied in breast cancer, some of which have been observed in Gene Regulatory Networks (GRNs). In this work we examine the patterns and features of a GRN composed of transcription factors (TFs) in MCF-7 breast cancer cell lines, providing valuable information regarding breast cancer. In particular, some genes whose αi ∗ associated parameter values revealed extreme positive and negative values, and, as such, can be identified as breast cancer prediction genes. We indicate that the PKN2, MKL1, MED23, CUL5 and GLI genes demonstrate a tumor suppressor profile, and that the MTR, ITGA2B, TELO2, MRPL9, MTTL1, WIPI1, KLHL20, PI4KB, FOLR1 and SHC1 genes demonstrate an oncogenic profile. We propose that these may serve as potential breast cancer prediction genes, and should be prioritized for further clinical studies on breast cancer. This new model allows for the assignment of values to the αi ∗ parameters associated with gene expression. It was noted that some αi ∗ parameters are associated with genes previously described as breast cancer biomarkers, as well as other genes not yet studied in relation to this disease.


Asunto(s)
Neoplasias de la Mama/genética , Regulación Neoplásica de la Expresión Génica/genética , Redes Reguladoras de Genes/genética , Biomarcadores de Tumor/genética , Línea Celular Tumoral , Progresión de la Enfermedad , Femenino , Perfilación de la Expresión Génica/métodos , Humanos , Modelos Logísticos , Células MCF-7 , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Factores de Transcripción/genética
3.
Biochem Genet ; 58(1): 74-101, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31273557

RESUMEN

Chromosomal microarray (CMA) has emerged as a robust tool for identifying microdeletions and microduplications, termed copy number variants (CNVs). Nevertheless, data regarding its utility in different patient populations with developmental delay (DD), dysmorphic features (DF) and congenital anomalies (CA), is a matter of dense debate. Although regions of homozygosity (ROH) are not diagnostic of a specific condition, they may have pathogenic implications. Certain CNVs and ROH have ethnically specific occurrences and frequencies. We aimed to determine whether CMA testing offers additional diagnostic information over classical cytogenetics for identifying genomic imbalances in a pediatric cohort with idiopathic DD, DF, or CA. One hundred sixty-nine patients were offered cytogenetics and CMA simultaneously for etiological diagnosis of DD (n = 67), DF (n = 52) and CA (n = 50). CMA could identify additional, clinically significant anomalies as compared with cytogenetics. CMA detected 61 CNVs [21 (34.4%) pathogenic CNVs, 37 (60.7%) variants of uncertain clinical significance and 3 (4.9%) benign CNVs] in 44 patients. CMA identified one or more ROH in 116/169 (68.6%) patients. When considering pathogenic CNVs and aneuploidies as positive findings, 9/169 (5.3%) received a genetic diagnosis from cytogenetics, while 25/169 (14.8%) could have a genetic diagnosis from CMA. The identification of ROH was clinically significant in two cases (2/169), thereby, adding 1.2% to the diagnostic yield of CMA (16% vs. 5.3%, p < 0.001). CMA uncovers additional genetic diagnoses over cytogenetics, thereby, offering a much higher diagnostic yield. Our findings convincingly demonstrate the additive diagnostic value of clinically significant ROH identified during CMA testing, highlighting the need for careful clinical interpretation of these ROH.


Asunto(s)
Síndrome de Down/diagnóstico , Homocigoto , Síndrome de Klinefelter/diagnóstico , Síndrome de la Trisomía 13/diagnóstico , Síndrome de la Trisomía 18/diagnóstico , Síndrome de Turner/diagnóstico , Adolescente , Niño , Preescolar , Rotura Cromosómica , Estudios de Cohortes , Variaciones en el Número de Copia de ADN , Discapacidades del Desarrollo/genética , Síndrome de Down/genética , Femenino , Humanos , Lactante , Recién Nacido , Síndrome de Klinefelter/genética , Masculino , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Síndrome de la Trisomía 13/genética , Síndrome de la Trisomía 18/genética , Síndrome de Turner/genética
4.
J Sci Food Agric ; 100(1): 325-334, 2020 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-31584699

RESUMEN

BACKGROUND: Meat fraud and adulteration incidents occur frequently in almost all regions of the globe, especially with the increase in the world's population. To ensure the authenticity of meat products, we developed a 10-plex xMAP assay to simultaneously detect ten animal materials: bovine, caprine, poultry, swine, donkey, deer, horse, dog, fox and mink. RESULTS: This method was investigated by analyzing DNA extracts from raw muscle, muscle mixtures, meat products and animal feeds. Our results indicated that the species of interest can be identified, differentiated and detected down to 1 g kg-1 in binary mixtures or 0.01-0.001 ng of genomic DNA from specific species. Testing of 125 commercial samples showed a 97.4% coincidence rate with the method used in routine testing in our lab. CONCLUSION: These results indicated that the method established in this study could detect ten animal materials simultaneously within 3 h, which provides a new, useful tool for animal ingredient analysis in meat products and animal feeds. © 2019 Society of Chemical Industry.


Asunto(s)
ADN Mitocondrial/genética , Contaminación de Alimentos/análisis , Productos de la Carne/análisis , Técnicas de Amplificación de Ácido Nucleico/métodos , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Alimentación Animal/análisis , Animales , Bovinos , Ciervos , Perros , Zorros , Cabras , Caballos , Visón , Técnicas de Amplificación de Ácido Nucleico/instrumentación , Aves de Corral , Porcinos
5.
BMC Bioinformatics ; 20(1): 625, 2019 Dec 03.
Artículo en Inglés | MEDLINE | ID: mdl-31795929

RESUMEN

BACKGROUND: Transcriptome analysis aims at gaining insight into cellular processes through discovering gene expression patterns across various experimental conditions. Biclustering is a standard approach to discover genes subsets with similar expression across subgroups of samples to be identified. The result is a set of biclusters, each forming a specific submatrix of rows (e.g. genes) and columns (e.g. samples). Relevant biclusters can, however, be missed when, due to the presence of a few outliers, they lack the assumed homogeneity of expression values among a few gene/sample combinations. The Max-Sum SubMatrix problem addresses this issue by looking at highly expressed subsets of genes and of samples, without enforcing such homogeneity. RESULTS: We present here the K-CPGC algorithm to identify K relevant submatrices. Our main contribution is to show that this approach outperforms biclustering algorithms to identify several gene subsets representative of specific subgroups of samples. Experiments are conducted on 35 gene expression datasets from human tissues and yeast samples. We report comparative results with those obtained by several biclustering algorithms, including CCA, xMOTIFs, ISA, QUBIC, Plaid and Spectral. Gene enrichment analysis demonstrates the benefits of the proposed approach to identify more statistically significant gene subsets. The most significant Gene Ontology terms identified with K-CPGC are shown consistent with the controlled conditions of each dataset. This analysis supports the biological relevance of the identified gene subsets. An additional contribution is the statistical validation protocol proposed here to assess the relative performances of biclustering algorithms and of the proposed method. It relies on a Friedman test and the Hochberg's sequential procedure to report critical differences of ranks among all algorithms. CONCLUSIONS: We propose here the K-CPGC method, a computationally efficient algorithm to identify K max-sum submatrices in a large gene expression matrix. Comparisons show that it identifies more significantly enriched subsets of genes and specific subgroups of samples which are easily interpretable by biologists. Experiments also show its ability to identify more reliable GO terms. These results illustrate the benefits of the proposed approach in terms of interpretability and of biological enrichment quality. Open implementation of this algorithm is available as an R package.


Asunto(s)
Genes , Algoritmos , Análisis por Conglomerados , Bases de Datos Genéticas , Ontología de Genes , Humanos , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Saccharomyces cerevisiae/genética
6.
Anticancer Res ; 39(12): 6457-6462, 2019 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-31810909

RESUMEN

BACKGROUND/AIM: Nicotinamide phosphoribosyltransferase (NAMPT), a key enzyme in the NAD+ biosynthetic pathway, is a drug target of potent anticancer candidates, including FK866 and other reported NAMPT inhibitors. However, it is known that NAMPT point-mutations render resistance to specific NAMPT inhibitors in several cancer cells. We investigated the resistance mechanisms of NAMPT inhibitor FK866 in human colorectal cancer (CRC) cells. MATERIALS AND METHODS: We used CRC human cell line HCT116 to determine the expression profiles of FK866-sensitive parental HCT116 cells and FK866-resistant HCT116 (HCT116RFK866) cells by DNA microarray analysis. The levels of multidrug resistance protein 1 (MDR1) were assessed via western blot. In addition, we analyzed the sensitivity of FK866 in parental HCT116 cells and HCT116RFK866 cells by co-treatment with MDR1 inhibitor verapamil. RESULTS: Our results revealed an association between ATP-binding cassette (ABC) transporter gene ABCB1 and resistance to NAMPT inhibitor FK866 in both HCT116RFK866 cells and parental HCT116 cells. The expression of ABCB1, which encodes MDR1, was lower in HCT116RFK866 cells than in parental HCT116 cells. Furthermore, the protein level of MDR1/ATP-binding cassette sub-family B member 1 (ABCB1) was 0.5-fold lower in HCT116RFK866 cells than in parental HCT116 cells. Additionally, HCT116RFK866 cells showed improved sensitivity to FK866 when co-treated with verapamil, an ABCB1 inhibitor. Interestingly, the efficacy of FK866 in parental HCT116 cells was the same for the treatment with FK866 alone or in combination with verapamil. CONCLUSION: The change in expression of ABCB1 plays a key role in CRC drug resistance to NAMPT inhibitor FK866. This suggests that the MDR1/ABCB1 mechanism may regulate the resistance of anticancer NAMPT inhibitor FK866.


Asunto(s)
Neoplasias Colorrectales/genética , Resistencia a Antineoplásicos , Subfamilia B de Transportador de Casetes de Unión a ATP/genética , Subfamilia B de Transportador de Casetes de Unión a ATP/metabolismo , Acrilamidas/farmacología , Neoplasias Colorrectales/metabolismo , Citocinas/antagonistas & inhibidores , Regulación hacia Abajo , Sinergismo Farmacológico , Perfilación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica , Células HCT116 , Humanos , Nicotinamida Fosforribosiltransferasa/antagonistas & inhibidores , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Piperidinas/farmacología , Verapamilo/farmacología
7.
PLoS Comput Biol ; 15(11): e1007509, 2019 11.
Artículo en Inglés | MEDLINE | ID: mdl-31756191

RESUMEN

The prevailing paradigm for the analysis of biological data involves comparing groups of replicates from different conditions (e.g. control and treatment) to statistically infer features that discriminate them (e.g. differentially expressed genes). However, many situations in modern genomics such as single-cell omics experiments do not fit well into this paradigm because they lack true replicates. In such instances, spectral techniques could be used to rank features according to their degree of consistency with an underlying metric structure without the need to cluster samples. Here, we extend spectral methods for feature selection to abstract simplicial complexes and present a general framework for clustering-independent analysis. Combinatorial Laplacian scores take into account the topology spanned by the data and reduce to the ordinary Laplacian score when restricted to graphs. We demonstrate the utility of this framework with several applications to the analysis of gene expression and multi-modal genomic data. Specifically, we perform differential expression analysis in situations where samples cannot be grouped into distinct classes, and we disaggregate differentially expressed genes according to the topology of the expression space (e.g. alternative paths of differentiation). We also apply this formalism to identify genes with spatial patterns of expression using fluorescence in-situ hybridization data and to establish associations between genetic alterations and global expression patterns in large cross-sectional studies. Our results provide a unifying perspective on topological data analysis and manifold learning approaches to the analysis of large-scale biological datasets.


Asunto(s)
Biología Computacional/métodos , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Algoritmos , Análisis por Conglomerados , Perfilación de la Expresión Génica/métodos , Genómica/métodos , Modelos Teóricos
8.
Int J Mol Sci ; 20(20)2019 Oct 11.
Artículo en Inglés | MEDLINE | ID: mdl-31614589

RESUMEN

MADS-box genes play a pivotal role in various processes, including floral and seed development, controlling flowering time, regulation of fruits ripening, and respond to abiotic and biotic stressors in planta. Tobacco (Nicotiana tabacum) has been widely used as a model plant for analyzing the gene function, however, there has been less information on the regulation of flowering, and the associated genes. In the present study, a total of 168 NtMADS-box genes were identified from tobacco, and their phylogenetic relationship, chromosome locations, and gene structures were further analyzed. NtMADS-box genes can be clustered into four sub-families of Mα, Mγ, MIKC*, and MIKCC. A total of 111 NtMADS-box genes were distributed on 20 chromosomes, and 57 NtMADS-box genes were located on the unanchored scaffolds due to the complex and incomplete assembly of the tobacco genome. Expression profiles of NtMADS-box genes by microarray from 23 different tissues indicated that members in different NtMADS-box gene subfamilies might play specific roles in the growth and flower development, and the transcript levels of 24 NtMADS-box genes were confirmed by quantitative real-time PCR. Importantly, overexpressed NtSOC1/NtMADS133 could promote early flowering and dwarfism in transgenic tobacco plants. Therefore, our findings provide insights on the characterization of NtMADS-box genes to further study their functions in plant development.


Asunto(s)
Perfilación de la Expresión Génica/métodos , Proteínas de Dominio MADS/genética , Análisis de Secuencia de ADN/métodos , Tabaco/crecimiento & desarrollo , Mapeo Cromosómico , Evolución Molecular , Regulación del Desarrollo de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Familia de Multigenes , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Filogenia , Proteínas de Plantas/genética , Tabaco/genética
9.
Cancer Invest ; 37(9): 440-452, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31530033

RESUMEN

Ovarian cancer is the deadliest gynecologic cancer. The large-scale microRNA (miRNA) expression profiling and individual miRNA validation was performed to find potential novel biomarkers for ovarian cancer. The most consistent overexpression of miRs-200b-3p, 135 b-5p and 182-5p was found in both ascitic fluid and tumors and suggests their potential as oncogenes. miR-451a was consistently underexpressed so may be a tumor suppressor. Results were inconsistent for miR-204-5p, which was overexpressed in ascitic fluid but underexpressed in tumor tissue. miR-203a-3p was generally overexpressed but this failed to be proved in independent sample set in tissue validation.


Asunto(s)
Líquido Ascítico/química , Biomarcadores de Tumor/genética , Perfilación de la Expresión Génica/métodos , MicroARNs/genética , Neoplasias Ováricas/genética , Ovario/química , Anciano , Femenino , Regulación Neoplásica de la Expresión Génica , Humanos , Persona de Mediana Edad , Estadificación de Neoplasias , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Neoplasias Ováricas/patología , Pronóstico
10.
Anal Bioanal Chem ; 411(25): 6745-6754, 2019 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-31482291

RESUMEN

In the literature, there are reports of the utilization of various hydrogels to create generic platforms for protein microarray applications. Here, a novel strategy was developed to obtain high-performance microarrays. In it, a dextran hydrogel is used to covalently immobilize oligonucleotides and proteins. This method employs aqueous solutions of dextran methacrylate (Dx-MA), which is a biocompatible photopolymerizable monomer. Capture probes are immobilized inside the hydrogel via a light-induced thiol-acrylate coupling reaction at the same time as the dextran polymer is formed. Hydrogel microarrays based on this technique were prepared on different surfaces, such as a Blu-ray Disk and polycarbonate or alkene-functionalized glass slides, and these systems showed high probe-loading capabilities and good biorecognition yields. This methodology presents advantages such as a low cost, a short analysis time, a low limit of detection, and multiplexing capabilities, among others. Confocal fluorescence microscopy analysis demonstrated that in these hydrogel-based microarrays, receptor immobilization and the biorecognition event occurred within the hydrogel and not merely on the surface.


Asunto(s)
Dextranos/química , Ácidos Nucleicos Inmovilizados/química , Metacrilatos/química , Química Clic/métodos , Hidrogeles/química , Ácidos Nucleicos/análisis , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Cemento de Policarboxilato/química , Compuestos de Sulfhidrilo/química
11.
Intervirology ; 62(3-4): 124-133, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31487743

RESUMEN

BACKGROUND: Cervical cancer is caused by a persistent infection of human papillomavirus (HPV). Therefore, tests which detect the carcinogenic virus can be used for cervical cancer screening. OBJECTIVE: This is the first evaluation of the HPV DNA Array (AID Diagnostika, Strassberg, Germany), an E1-based genotyping polymerase chain reaction (PCR) test for identification of 29 HPV types (6, 11, 16, 18, 26, 31, 33, 35, 39, 40, 42, 44, 45, 51, 52, 53, 54, 56, 58, 59, 66, 67, 68, 69, 70, 73, 82, 85, and 97). METHODS: Analytical performance of the assay was assessed with cervical cancer cell lines with known HPV status, and preselected clinical cervical scrapings genotyped by multiplexed genotyping (MPG) with a Luminex readout (validated in-house assay). Intra- and inter-laboratory reproducibility experiments were performed to ensure the reliability of the assay. RESULTS: HPV DNA Array identified the intrinsic HPV genotype in all cervical cancer cell lines and demonstrated a high sensitivity for HPV16 probe (1 cell per PCR reaction), as well as HPV18 and 45 probes (100 cells per PCR reaction). When compared with MPG, HPV DNA Array showed a good agreement of 92.2% for HPV detection irrespective of type (κ = 0.601), and demonstrated high agreement for HPV16 (80.7%, κ = 0.836) and HPV18 (86.7%, κ = 0.925). Furthermore, high intra-/inter-laboratory reproducibility was observed (90.9-100%). CONCLUSION: HPV DNA Array showed high sensitivity for correct HPV genotype detection in experimental and clinical samples with a good correlation to the reference test. Since HPV DNA Array is based on a simple multiplexed PCR followed by reverse hybridization in a 96-well format and automated visual readout by AID ELISpot reader, it is capable of high throughput in a time-effective manner. HPV DNA Array could be considered for extended HPV genotyping of cervical smears.


Asunto(s)
Genotipo , Técnicas de Genotipaje/métodos , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Proteínas Oncogénicas Virales/genética , Papillomaviridae/clasificación , Papillomaviridae/genética , Infecciones por Papillomavirus/virología , Línea Celular Tumoral , Humanos , Papillomaviridae/aislamiento & purificación , Reproducibilidad de los Resultados , Sensibilidad y Especificidad
12.
Cancer Sci ; 110(10): 3204-3214, 2019 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-31385416

RESUMEN

Peritoneal dissemination is the most frequent metastatic route of ovarian cancer. However, due to the high heterogeneity in ovarian cancer, most conventional studies lack parental tumor controls relevant to metastases and, thus, it is difficult to trace the molecular changes of cancer cells along with the selection by the abdominal microenvironment. Here, we established an in vivo mouse peritoneal dissemination scheme that allowed us to select more aggressive sublines from parental ovarian cancer cells, including A2780 and SKOV-3. Microarray and gene profiling analyses indicated that autophagy-related genes were enriched in selected malignant sublines. Detection of LC3-II, p62 and autophagic puncta demonstrated that these malignant variants were more sensitive to autophagic induction when exposed to diverse stress conditions, such as high cell density, starvation and drug treatment. As compared with parental A2780, the selected variant acquired the ability to grow better under high-density stress; however, this effect was reversed by addition of autophagic inhibitors or knockdown of ATG5. When analyzing the clinical profiles of autophagy-related genes identified to be enriched in malignant A2780 variant, 73% of them had prognostic significance for the survival of ovarian cancer patients. Taken together, our findings indicate that an increase in autophagic potency among ovarian cancer cells is crucial for selection of metastatic colonies in the abdominal microenvironment. In addition, the derived autophagic gene profile can not only predict prognosis well but can also be potentially applied to precision medicine for identifying those ovarian cancer patients suitable for taking anti-autophagy cancer drugs.


Asunto(s)
Proteínas Relacionadas con la Autofagia/genética , Perfilación de la Expresión Génica/métodos , Proteínas Asociadas a Microtúbulos/genética , Neoplasias Ováricas/patología , Neoplasias Peritoneales/secundario , Proteínas de Unión al ARN/genética , Animales , Autofagia , Línea Celular Tumoral , Supervivencia Celular , Femenino , Humanos , Ratones , Trasplante de Neoplasias , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Neoplasias Ováricas/genética , Neoplasias Ováricas/metabolismo , Neoplasias Peritoneales/genética , Neoplasias Peritoneales/patología , Medicina de Precisión , Pronóstico , Microambiente Tumoral
13.
Clin Lab ; 65(8)2019 Aug 01.
Artículo en Inglés | MEDLINE | ID: mdl-31414744

RESUMEN

BACKGROUND: Recently, long non-coding RNAs (lncRNAs) have attracted substantial attention owing to their unforeseen critical roles in a wide range of biological processes. The aim of our study was to provide an overview of lncRNA expression profiles in plasma of RA patients. METHODS: The Agilent LncRNA + mRNA Human Gene Expression Microarray V4.0 was employed to determine differentially expressed (DE) lncRNAs and mRNAs in plasma of four female newly diagnosed and DMARD-naïve RA patients and four female age-matched healthy controls. The KOBAS (KEGG Orthology Based Annotation System) software was applied to determine the gene ontology (GO) terms and pathway in which the DE mRNAs were enriched. Furthermore, a lncRNA-mRNA co-expression network was constructed according to the correlation between DE lncRNAs and mRNAs. RESULTS: Compared with healthy controls, a total of 289 DE lncRNAs (169 up-regulated and 120 down-regulated) and 468 DE mRNAs (280 up-regulated and 188 down-regulated) were found in the plasma of patients with RA. Bioinformatics analysis indicated that the DE mRNAs might be involved in the pathogenesis of RA mainly through platelets. In addition, a co-expression network composed of 229 network nodes and 340 connections between 116 lncRNAs and 113 mRNAs was constructed. CONCLUSIONS: We characterized the plasma lncRNA expression profiles in RA patients for the first time. Our results could shed new light on the pathogenesis of RA and help identify lncRNAs as novel diagnostic biomarkers and therapeutic targets for RA.


Asunto(s)
Artritis Reumatoide/genética , Biomarcadores/metabolismo , Perfilación de la Expresión Génica/métodos , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , ARN Largo no Codificante/genética , Adulto , Artritis Reumatoide/sangre , Artritis Reumatoide/diagnóstico , Biomarcadores/sangre , Biología Computacional , Femenino , Ontología de Genes , Redes Reguladoras de Genes/genética , Humanos , Persona de Mediana Edad , ARN Largo no Codificante/sangre , ARN Mensajero/sangre , ARN Mensajero/genética , Transducción de Señal/genética
14.
Int J Pediatr Otorhinolaryngol ; 126: 109630, 2019 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-31442870

RESUMEN

OBJECTIVES: More than 50% of congenital hearing loss is attributed to genetic factors. Data of gene mutation associated with hearing loss from large population studies in Chinese population are scarce. In this study, we conducted a comprehensive newborn genetic screening in China to establish the carrier frequency and mutation spectrum of deafness-associated genes. METHODS: A total of 53,033 newborns were screened for hearing defects associated mutations. Twenty hot spot mutations in GJB2, GJB3, SLC26A4 and mitochondria12S rRNA were examined using suspension array analysis. RESULTS: 14,185 newborns (26.75%) were identified with at least one mutated allele. 872 (1.64%) neonates carried homozygous mutations including 112 (0.21%) mitochondrial DNA homoplasmy, 228 (0.43%) were compound heterozygotes, and 11,985 (22.59%) were heterozygotes including 11 (0.02%) mitochondrial DNA heteroplasmy. Top five mutations included 109 G > A, 235 delC, 299-300 delAT in GJB2, IVS7-2 A > G in SLC26A4 and 1555 A > G in mitochondria12S rRNA. Notably, a total of 10,995 neonates (20.73%) carried 109 G > A in GJB2. Moreover, the allele frequencies of 109 G > A were detected 11.61% in Guangdong, 10.44% in Sichuan and 2.88% in Shandong, respectively, a significant difference in prevalence among these geographic regions (p<0.01). In addition, the high frequency of 109 G > A in GJB2 was confirmed by a TaqMan probe-based qPCR assay. Very recently, the ClinGen Hearing Loss Expert Panel reached a consensus and confirmed its pathogenic role in hearing impairment. CONCLUSION: We delineated the mutation profile of common deafness-causing genes in the Chinese population and highlighted the high prevalence of 109 G > A pathogenic mutation. Our study may facilitate early diagnosis/intervention and genetic counseling for hearing impairment in clinical practice.


Asunto(s)
Conexinas/genética , Sordera/genética , Pruebas Genéticas , Mutación , Tamizaje Neonatal , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Grupo de Ascendencia Continental Asiática/genética , China/epidemiología , Sordera/congénito , Sordera/epidemiología , Femenino , Frecuencia de los Genes , Heterocigoto , Homocigoto , Humanos , Recién Nacido , Masculino , Mitocondrias/genética , Prevalencia , ARN Ribosómico/genética , Transportadores de Sulfato/genética
16.
Molecules ; 24(13)2019 Jun 28.
Artículo en Inglés | MEDLINE | ID: mdl-31261664

RESUMEN

Obesity is a serious health problem, while the current anti-obesity drugs are not very effective. The Connectivity Map (C-Map), an in-silico drug screening approach based on gene expression profiles, has recently been indicated as a promising strategy for drug repositioning. In this study, we performed mRNA expression profile analysis using microarray technology and identified 435 differentially expressed genes (DEG) during adipogenesis in both C3H10T1/2 and 3T3-L1 cells. Then, DEG signature was uploaded into C-Map, and using pattern-matching methods we discovered that pyrvinium, a classical anthelminthic, is a novel anti-adipogenic differentiation agent. Pyrvinium suppressed adipogenic differentiation in a dose-dependent manner, as evidenced by Oil Red O staining and the mRNA levels of adipogenic markers. Furthermore, we identified that the inhibitory effect of pyrvinium was resulted primarily from the early stage of adipogenesis. Molecular studies showed that pyrvinium downregulated the expression of key transcription factors C/EBPa and PPARγ. The mRNA levels of notch target genes Hes1 and Hey1 were obviously reduced after pyrvinium treatment. Taken together, this study identified many differentially expressed genes involved in adipogenesis and demonstrated for the first time that pyrvinium is a novel anti-adipogenic compound for obesity therapy. Meanwhile, we provided a new strategy to explore potential anti-obesity drugs.


Asunto(s)
Adipogénesis/efectos de los fármacos , Antihelmínticos/farmacología , Perfilación de la Expresión Génica/métodos , Compuestos de Pirvinio/farmacología , Células 3T3-L1 , Animales , Diferenciación Celular/efectos de los fármacos , Línea Celular , Relación Dosis-Respuesta a Droga , Reposicionamiento de Medicamentos , Regulación de la Expresión Génica/efectos de los fármacos , Ratones , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos
17.
BMC Vet Res ; 15(1): 253, 2019 Jul 19.
Artículo en Inglés | MEDLINE | ID: mdl-31324180

RESUMEN

BACKGROUND: Avian influenza virus (AIV), infectious bronchitis virus (IBV), and Newcastle disease virus (NDV) are important avian pathogens that can cause enormous economic loss on the poultry industry. Different respiratory etiological agents may induce similar clinical signs that make differential diagnosis difficult. Importantly, AIV brings about severe threat to human public health. Therefore, a novel method that can distinguish these viruses quickly and simultaneously is urgently needed. RESULTS: In this study, an oligonucleotide microarray system was developed. AIV, including H5, H7, and H9 subtypes; NDV; and IBV were simultaneously detected and differentiated on a microarray. Three probes specific for AIV, NDV, and IBV, as well as three other probes for differentiating H5, H7, and H9 of AIV, were first designed and jet-printed to predetermined locations of initiator-integrated poly(dimethylsiloxane) for the synchronous detection of the six pathogens. The marked multiplex reverse transcription polymerase chain reaction (PCR) products were hybridized with the specific probes, and the results of hybridization were read directly with the naked eyes. No cross-reaction was observed with 10 other subtypes of AIV and infectious bursal disease virus, indicating that the oligonucleotide microarray assay was highly specific. The sensitivity of the method was at least 100 times higher than that of the conventional PCR, and the detection limit of NDV, AIV, H5, H7, and H9 can reach 0.1 EID50 (50% egg infective dose), except that of IBV, which was 1 EID50 per reaction. In the validation of 93 field samples, AIV, IBV, and NDV were detected in 53 (56.99%) samples by oligonucleotide microarray and virus isolation and in 50 (53.76%) samples by conventional PCR. CONCLUSIONS: We have successfully developed an approach to differentiate AIV, NDV, IBV, H5, H7, and H9 subtypes of AIV using oligonucleotide microarray. The microarray is an accurate, high-throughput, and relatively simple method for the rapid detection of avian respiratory viral diseases. It can be used for the epidemiological surveillance and diagnosis of AIV, IBV, and NDV.


Asunto(s)
Virus de la Bronquitis Infecciosa/genética , Virus de la Influenza A/genética , Virus de la Enfermedad de Newcastle/genética , Análisis de Secuencia por Matrices de Oligonucleótidos/veterinaria , Enfermedades de las Aves de Corral/virología , Animales , Infecciones por Coronavirus/virología , Virus de la Enfermedad Infecciosa de la Bolsa/genética , Gripe Aviar/virología , Reacción en Cadena de la Polimerasa Multiplex/métodos , Reacción en Cadena de la Polimerasa Multiplex/veterinaria , Enfermedad de Newcastle/virología , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Aves de Corral , Sensibilidad y Especificidad
18.
BMC Genomics ; 20(Suppl 8): 549, 2019 Jul 16.
Artículo en Inglés | MEDLINE | ID: mdl-31307398

RESUMEN

BACKGROUND: By definition, effect of synonymous single-nucleotide variants (SNVs) on protein folding and function are neutral, as they alter the codon and not the encoded amino acid. Recent examples indicate tissue-specific and transfer RNA (tRNA)-dependent effects of some genetic variations arguing against neutrality of synonymous SNVs for protein biogenesis. RESULTS: We performed systematic analysis of tRNA abunandance across in various models used in cystic fibrosis (CF) research and drug development, including Fischer rat thyroid (FRT) cells, patient-derived primary human bronchial epithelia (HBE) from lung biopsies, primary human nasal epithelia (HNE) from nasal curettage, intestinal organoids, and airway progenitor-directed differentiation of human induced pluripotent stem cells (iPSCs). These were compared to an immortalized CF bronchial cell model (CFBE41o-) and two widely used laboratory cell lines, HeLa and HEK293. We discovered that specific synonymous SNVs exhibited differential effects which correlated with variable concentrations of cognate tRNAs. CONCLUSIONS: Our results highlight ways in which the presence of synonymous SNVs may alter local kinetics of mRNA translation; and thus, impact protein biogenesis and function. This effect is likely to influence results from mechansistic analysis and/or drug screeining efforts, and establishes importance of cereful model system selection based on genetic variation profile.


Asunto(s)
Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Polimorfismo de Nucleótido Simple , ARN de Transferencia/genética , Codón/genética , Regulador de Conductancia de Transmembrana de Fibrosis Quística/genética , Genotipo , Células HEK293 , Células HeLa , Humanos , Fenotipo
19.
Anal Chim Acta ; 1077: 297-304, 2019 Oct 24.
Artículo en Inglés | MEDLINE | ID: mdl-31307722

RESUMEN

In this study, we designed a fluorescence enhancement strategy based on silver nanoparticle (AgNP) aggregates for the detection of hepatitis B virus DNA sequences. AgNPs were functioned with recognition probes (Cy3-probe) and hybrid probes (Oligomer-A and Oligomer-B). The presence of target DNA mediated the formation of sandwich complexes between the immobilized capture probes and the functionalized AgNPs, which was followed by hybridization-induced formation of AgNP aggregates. The fluorescent intensity could be extremely amplified by both the increasing number of fluorophores and metal enhanced fluorescence (MEF) effect. Under optimal conditions, this method achieved a detection limit of 50 fM which was 1560-fold lower than that of un-enhanced fluorescent assays. It was illustrated that the HBV DNA concentrations ranging from 100 fM to 10 nM had a good log-linear correlation with the corresponding fluorescent intensity (R = 0.991). Moreover, this method had high specificity both for distinguishing single-base mismatches and identifying target DNA under the interference of genomic DNA. This fluorescent microarray had high-throughput analytical potential and could apply to many other disease diagnoses.


Asunto(s)
ADN Viral/análisis , Virus de la Hepatitis B/genética , Nanopartículas del Metal/química , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Plata/química , Sondas de ADN , ADN Viral/genética , Límite de Detección , Hibridación de Ácido Nucleico
20.
Cancer Sci ; 110(10): 3197-3203, 2019 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-31361379

RESUMEN

Intrahepatic cholangiocarcinoma is a rare malignant biliary neoplasm that causes a poor prognosis even after curative hepatectomy. Liver metastasis is the major recurrence pattern of intrahepatic cholangiocarcinoma; therefore, the prevention of liver metastasis is a desirable objective. The aim of this study is to identify gene(s) related to liver metastasis of intrahepatic cholangiocarcinoma and to examine the inhibitory effects on metastasis of intrahepatic cholangiocarcinoma by controlling such gene(s). We collected 3 pairs of intrahepatic cholangiocarcinoma frozen samples, and 36 pairs (primary and metastatic lesions) of intrahepatic cholangiocarcinoma formalin-fixed paraffin-embedded samples, from patients who underwent surgical resection at hospitals related to the Kyushu Study Group of Liver Surgery between 2002 and 2016. We carried out cDNA microarray analyses and immunohistochemistry to identify candidate genes, and evaluated one of them as a therapeutic target using human cholangiocarcinoma cell lines. We identified 4 genes related to liver metastasis using cDNA microarray, and found that CXCL12 was the only gene whose expression was significantly higher in liver metastasis than in primary intrahepatic cholangiocarcinoma by immunohistochemistry (P = .003). In prognosis, patients in the high CXCL12 group showed a significantly poor prognosis in disease-free (P < .0001) and overall survival (P = .0004). By knockdown of CXCL12, we could significantly suppress the invasive and migratory capabilities of 2 human cholangiocarcinoma cell lines. Therefore, CXCL12 might be associated with metastasis and poor prognosis in intrahepatic cholangiocarcinoma.


Asunto(s)
Neoplasias de los Conductos Biliares/patología , Quimiocina CXCL12/genética , Quimiocina CXCL12/metabolismo , Colangiocarcinoma/patología , Neoplasias Hepáticas/secundario , Anciano , Neoplasias de los Conductos Biliares/genética , Neoplasias de los Conductos Biliares/metabolismo , Línea Celular Tumoral , Movimiento Celular , Colangiocarcinoma/genética , Colangiocarcinoma/metabolismo , Femenino , Perfilación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica , Humanos , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/metabolismo , Neoplasias Hepáticas/patología , Persona de Mediana Edad , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Pronóstico , Regulación hacia Arriba
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