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1.
Medicine (Baltimore) ; 98(37): e17156, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31517861

RESUMO

This study aims to screen differentially expressed host miRNAs that could be used as diagnostic markers for liver alveolar echinococcosis (LAE).Differentially expressed miRNAs were first screened by miRNA microarray in liver tissues from2 LAE patients and normal liver tissues from 3 LAE patients, followed by qRT-PCR validation in 15 LAE tissues and 15 normal tissues. Target genes of differentially expressed miRNAs were predicted using Targetscan, PITA and microRNAorg database, and the overlapped predicted target genes were analyzed by GO and KEGG.The hsa-miR-1237-3p, hsa-miR-33b-3p, and hsa-miR-483-3p were up-regulated whereas the hsa-miR-4306 was down-regulated in LAE tissues compared with normal controls (P < .05). The expression change of miR-483-3p was further confirmed in both liver tissues and plasma. Several predicted targets of miR-1237-3p, miR-4306, and miR-483-3p were related to DNA-dependent transcriptional regulation, developmental regulation of multicellular organisms, and biological functions such as cellular immune responses (T cell proliferation). The overlapped predicted target genes of the 4 differentially expressed miRNAs were enriched in mRNA surveillance, cancer signaling pathway, intestinal immune network, and other signal pathways.Our results indicate that miR-483-3p is a potential marker for the diagnosis of LAE, and targets of this miRNA could be the focus of further studies.


Assuntos
Equinococose Hepática/metabolismo , Fígado/metabolismo , MicroRNAs/metabolismo , Adulto , Biomarcadores/metabolismo , Feminino , Expressão Gênica , Humanos , Masculino , Análise em Microsséries , Pessoa de Meia-Idade
2.
Arch Virol ; 164(11): 2699-2706, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31435867

RESUMO

Recently, a clinical need for an improved human papilloma virus (HPV) test that covers a broad range of genotypes has emerged as a valuable primary screening tool for cervical lesions. The liquid bead microarray (LBMA) assay is a recently developed high-throughput platform covering a broad range of genotypes. Here, we compared the clinical performance of two recently developed LBMA assays, GeneFinderTM HPV Liquid Bead Microarray (GeneFinder) and CareGENETM HPV genotyping kit-O (CareGENE), in the Korean general population. A total of 3,148 cervical swabs were tested by the GeneFinder and CareGENE assays. Cases with discrepant results between the two assays were subjected to direct sequencing as a reference method for evaluating the performance of the two LBMA assays. Among all swabs tested, 12.6% showed HPV positivity, and the prevalent HPV genotypes were HPV53, 70, 16, 39, and 51, in that order. The concordance rates between the two assays for the detection of HPV and for genotyping were 96.6% (kappa = 0.836) and 94.5% (kappa = 0.779), respectively. The two LBMA assays showed comparable sensitivity and specificity for HPV detection (GeneFinder: sensitivity 94.4% and specificity 98.7%, CareGENE: sensitivity 89.8% and specificity 99.6%) and for genotyping (GeneFinder: sensitivity 91.0% and specificity 96.6%, CareGENE: sensitivity 90.2% and specificity 99.1%). This is the first demonstration that CareGENE has comparable clinical performance to GeneFinder, which has been established to show excellent performance for screening HPV in previous studies. Both LBMA platforms are thus considered to be valuable tools for HPV detection and genotyping to improve cervical screening in the general population.


Assuntos
Alphapapillomavirus/genética , Detecção Precoce de Câncer/métodos , Ensaios de Triagem em Larga Escala/métodos , Análise em Microsséries/métodos , Infecções por Papillomavirus/diagnóstico , Neoplasias do Colo do Útero/diagnóstico , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Alphapapillomavirus/classificação , Alphapapillomavirus/isolamento & purificação , Feminino , Técnicas de Genotipagem , Humanos , Programas de Rastreamento/métodos , Pessoa de Meia-Idade , Sensibilidade e Especificidade , Neoplasias do Colo do Útero/virologia , Adulto Jovem
3.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 36(8): 773-776, 2019 Aug 10.
Artigo em Chinês | MEDLINE | ID: mdl-31400125

RESUMO

OBJECTIVE: To discuss the value of chromosomal microarray analysis (CMA) for the identification of DMD gene deletions during prenatal diagnosis. METHODS: G-banded karyotyping and CMA were performed on fetuses with ultrasonographic soft markers but no family history for Duchenne/Becker muscular dystrophy (DMD/BMD). Denaturing high-performance liquid chromatograghy (DHPLC) was used to detect DMD gene mutations in umbilical cord blood and peripheral blood samples from the mothers. RESULTS: For fetus 1, analysis of amniocytes showed a normal karyotype, while CMA detected a 119 kb deletion at Xp21.1 (32 565 489 - 32 681 461), which encompassed exons 10 to 16 of the DMD gene. The result was confirmed by DHPLC analysis. The mother was found to have loss of heterozygosity in the same region. For fetus 2, karyotyping of amniocytes also showed a normal male karyotype, while CMA detected a 254 kb deletion at Xp21.1 (32 104 604 - 32 358 874), which encompassed exons 41 to 44 of the DMD gene. The same deletion was not detected in the mother. DHPLC analysis confirmed the presence of both deletions. CONCLUSION: Two fetuses harboring DMD gene deletions but without a family history were discovered. CMA can improve the efficiency for detecting single gene diseases caused by deletions.


Assuntos
Distrofina/genética , Deleção de Genes , Achados Incidentais , Análise em Microsséries , Distrofia Muscular de Duchenne/genética , Éxons , Feminino , Feto , Humanos , Masculino , Gravidez
4.
Braz J Med Biol Res ; 52(8): e8522, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31365696

RESUMO

Pancreaticobiliary maljunction (PBM) is associated with high risk of epithelial atypical growth and malignant transformation of the bile duct or gallbladder. However, overall changes in genetic expression have not been examined in children with PBM. Genome-wide expression was analyzed using peripheral blood samples from 10 children with PBM and 15 pediatric controls. Differentially expressed genes (DEGs) were identified using microarray. Bioinformatics analysis was conducted using Gene Ontology and KEGG analyses. The top 5 in the up-regulated genes in PBM were verified with qRT-PCR. Receiver operator characteristic curve analysis was conducted to evaluate the predictive accuracy of selected genes for PBM. The microarray experiments identified a total of 876 DEGs in PBM, among which 530 were up-regulated and the remaining 346 were down-regulated. Verification of the top 5 up-regulated genes (TYMS, MYBPC1, FUT1, XAGE2, and GREB1L) by qRT-PCR confirmed the up-regulation of MYBPC1 and FUT1. Receiver operating characteristic curve analysis suggested that FUT1 and MYBPC1 up-regulation could be used to predict PBM, with the area under the curve of 0.873 (95%CI=0.735-1.000) and 0.960 (95%CI=0.891-1.000), respectively. FUT1 and MYBPC1 were up-regulated in children with PBM, and could be used as potential biomarkers for PBM.


Assuntos
Ductos Biliares/anormalidades , Proteínas de Transporte/genética , Fucosiltransferases/genética , Perfilação da Expressão Gênica , Ductos Pancreáticos/anormalidades , Regulação para Cima/genética , Neoplasias dos Ductos Biliares/etiologia , Estudos de Casos e Controles , Criança , Pré-Escolar , Dilatação Patológica/complicações , Dilatação Patológica/congênito , Feminino , Neoplasias da Vesícula Biliar/etiologia , Humanos , Lactente , Masculino , Análise em Microsséries
6.
Medicine (Baltimore) ; 98(27): e16225, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31277135

RESUMO

MicroRNAs (miRNAs) play a great contribution to the development of diabetic nephropathy (DN). The aim of this study was to explore potential miRNAs-genes regulatory network and biomarkers for the pathogenesis of DN using bioinformatics methods.Gene expression profiling data related to DN (GSE1009) was obtained from the Gene Expression Omnibus (GEO) database, and then differentially expressed genes (DEGs) between DN patients and normal individuals were screened using GEO2R, followed by a series of bioinformatics analyses, including identifying key genes, conducting pathway enrichment analysis, predicting and identifying key miRNAs, and establishing regulatory relationships between key miRNAs and their target genes.A total of 600 DEGs associated with DN were identified. An additional 7 key DEGs, including 6 downregulated genes, such as vascular endothelial growth factor α (VEGFA) and COL4A5, and 1 upregulated gene (CCL19), were identified in another dataset (GSE30528) from glomeruli samples. Pathway analysis showed that the down- and upregulated DEGs were enriched in 14 and 6 pathways, respectively, with 7 key genes mainly involved in extracellular matrix-receptor interaction, PI3K/Akt signaling, focal adhesion, and Rap1 signaling. The relationships between miRNAs and target genes were constructed, showing that miR-29 targeted COL4A and VEGFA, miR-200 targeted VEGFA, miR-25 targeted ITGAV, and miR-27 targeted EGFR.MiR-29 and miR-200 may play important roles in DN. VEGFA and COL4A5 were targeted by miR-29 and VEGFA by miR-200, which may mediate multiple signaling pathways leading to the pathogenesis and development of DN.


Assuntos
Biologia Computacional/métodos , Nefropatias Diabéticas/genética , Perfilação da Expressão Gênica/métodos , MicroRNAs/genética , Regulação para Cima , Redes Reguladoras de Genes , Humanos , Análise em Microsséries
7.
Medicine (Baltimore) ; 98(27): e16269, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31277149

RESUMO

Esophageal squamous cell carcinoma (ESCC) is a malignancy that severely threatens human health and carries a high incidence rate and a low 5-year survival rate. MicroRNAs (miRNAs) are commonly accepted as a key regulatory function in human cancer, but the potential regulatory mechanisms of miRNA-mRNA related to ESCC remain poorly understood.The GSE55857, GSE43732, and GSE6188 miRNA microarray datasets and the gene expression microarray datasets GSE70409, GSE29001, and GSE20347 were downloaded from Gene Expression Omnibus databases. The differentially expressed miRNAs (DEMs) and differentially expressed genes (DEGs) were obtained using GEO2R. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for DEGs were performed by Database for Annotation, Visualization and Integrated Discovery (DAVID). A protein-protein interaction (PPI) network and functional modules were established using the STRING database and were visualized by Cytoscape. Kaplan-Meier analysis was constructed based on The Cancer Genome Atlas (TCGA) database.In total, 26 DEMs and 280 DEGs that consisted of 96 upregulated and 184 downregulated genes were screened out. A functional enrichment analysis showed that the DEGs were mainly enriched in the ECM-receptor interaction and cytochrome P450 metabolic pathways. In addition, MMP9, PCNA, TOP2A, MMP1, AURKA, MCM2, IVL, CYP2E1, SPRR3, FOS, FLG, TGM1, and CYP2C9 were considered to be hub genes owing to high degrees in the PPI network. MiR-183-5p was with the highest connectivity target genes in hub genes. FOS was predicted to be a common target gene of the significant DEMs. Hsa-miR-9-3p, hsa-miR-34c-3p and FOS were related to patient prognosis and higher expression of the transcripts were associated with a poor OS in patients with ESCC.Our study revealed the miRNA-mediated hub genes regulatory network as a model for predicting the molecular mechanism of ESCC. This may provide novel insights for unraveling the pathogenesis of ESCC.


Assuntos
Biologia Computacional/métodos , Neoplasias Esofágicas/genética , Carcinoma de Células Escamosas do Esôfago/genética , Perfilação da Expressão Gênica/métodos , Regulação Neoplásica da Expressão Gênica , MicroRNAs/genética , RNA Neoplásico/genética , Bases de Dados Genéticas , Neoplasias Esofágicas/metabolismo , Carcinoma de Células Escamosas do Esôfago/metabolismo , Ontologia Genética , Redes Reguladoras de Genes , Humanos , Análise em Microsséries
8.
J Cancer Res Clin Oncol ; 145(9): 2383-2396, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31280346

RESUMO

PURPOSE: Breast cancer is one of the most common malignancies among females, and its prognosis is affected by a complex network of gene interactions. Weighted gene co-expression network analysis was used to construct free-scale gene co-expression networks and to identify potential biomarkers for breast cancer progression. METHODS: The gene expression profiles of GSE42568 were downloaded from the Gene Expression Omnibus database. RNA-sequencing data and clinical information of breast cancer from TCGA were used for validation. RESULTS: A total of ten modules were established by the average linkage hierarchical clustering. We identified 58 network hub genes in the significant module (R2 = 0.44) and 6 hub genes (AGO2, CDC20, CDCA5, MCM10, MYBL2, and TTK), which were significantly correlated with prognosis. Receiver-operating characteristic curve validated that the mRNA levels of these six genes exhibited excellent diagnostic efficiency in the test data set of GSE42568. RNA-sequencing data from TCGA showed that the expression levels of these six genes were higher in triple-negative tumors. One-way ANOVA suggested that these six genes were upregulated at more advanced stages. The results of independent sample t test indicated that MCM10 and TTK were associated with tumor size, and that AGO2, CDC20, CDCA5, MCM10, and MYBL2 were overexpressed in lymph-node positive breast cancer. CONCLUSIONS: AGO2, CDC20, CDCA5, MCM10, MYBL2, and TTK were identified as candidate biomarkers for further basic and clinical research on breast cancer based on co-expression analysis.


Assuntos
Biomarcadores Tumorais/genética , Neoplasias da Mama/diagnóstico , Neoplasias da Mama/genética , Redes Reguladoras de Genes , Transcriptoma , Biomarcadores Tumorais/análise , Neoplasias da Mama/mortalidade , Neoplasias da Mama/patologia , Análise por Conglomerados , Progressão da Doença , Feminino , Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica , Redes Reguladoras de Genes/genética , Ensaios de Triagem em Larga Escala , Humanos , Análise em Microsséries , Prognóstico
9.
J Cancer Res Clin Oncol ; 145(9): 2325-2333, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31317326

RESUMO

PURPOSE: Nodal positive lung adenocarcinoma includes wide range of survival. Several methods for the classification of nodal-positive lung cancer have been proposed. However, classification considering the impact of targetable genetic variants are lacking. The possibility of genetic variants for the better stratification of nodal positive lung adenocarcinoma was estimated. METHODS: Mutations of 36 genes between primary sites and metastatic lymph nodes (LNs) were compared using next-generation sequencing. Subsequently, mutations in EGFR and BRAF, rearrangements in ALK and ROS1 were evaluated in 69 resected pN1-2M0 adenocarcinoma cases. Recurrence-free survival (RFS), post-recurrence survival (PRS), and overall survival (OS) were evaluated with respect to targetable variants and tyrosine kinase inhibitor (TKI) therapy after recurrence. RESULTS: About 90% of variants were shared and allele frequencies were similar between primary and metastatic sites. In 69 pN1-2M0 cases, EGFR/ALK were positive in primary sites of 39 cases and same EGFR/ALK variants were confirmed in metastatic LNs of 96.7% tissue-available cases. Multivariate analyses indicated positive EGFR/ALK status was associated with worse RFS (HR 2.366; 95% CI 1.244-4.500; P = 0.009), and PRS was prolonged in cases receiving TKI therapy (no post-recurrence TKI therapies, HR 3.740; 95% CI 1.449-9.650; P = 0.006). OS did not differ with respect to targetable variants or TKI therapy. CONCLUSIONS: Cases harbouring targetable genetic variants had a higher risk of recurrence, but PRS was prolonged by TKI therapy. Classification according to the targetable genetic status provides a basis for predicting recurrence and determining treatment strategies after recurrence.


Assuntos
Adenocarcinoma de Pulmão/diagnóstico , Neoplasias Pulmonares/diagnóstico , Pulmão/metabolismo , Linfonodos/metabolismo , Mutação , Transcriptoma/genética , Adenocarcinoma de Pulmão/genética , Adenocarcinoma de Pulmão/patologia , Idoso , Idoso de 80 Anos ou mais , Análise Mutacional de DNA/métodos , Feminino , Regulação Neoplásica da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Pulmão/patologia , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patologia , Linfonodos/patologia , Metástase Linfática , Masculino , Análise em Microsséries/métodos , Pessoa de Meia-Idade , Recidiva Local de Neoplasia/genética , Prognóstico , Estudos Retrospectivos
10.
Medicine (Baltimore) ; 98(26): e16072, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31261517

RESUMO

Crohn disease (CD) is a multifactorial autoimmune disease which is characterized by chronic and recurrent gastrointestinal tract inflammatory disorder. However, the molecular mechanisms of CD remain unclear. Increasing evidences have demonstrated that circular RNAs (circRNAs) participate in the pathogenesis of a variety of disease and were considered as ideal biomarkers in human disease. This study aimed to investigate circRNA expression profiles and detect new biomarkers in inflammatory bowel disease (IBD). Differentially expression of circRNAs between CD and HCs (health controls) were screened by microarray analysis. Peripheral blood mononuclear cells (PBMCs) from 5 CD patients and 5 HCs were included in the microarray analysis. Then, the differences were validated by quantitative polymerase chain reaction (qPCR) following reverse transcription polymerase chain reaction (RT-PCR) in the patients of CD and sex- and age-matched HCs. The most differential expressed circRNA was further validated in ulcerative colitis (UC) patients. Statistical significance between CD, UC, and HCs was analyzed by Student t test for unpaired samples or one-way analysis of variance (ANOVA). Diagnostic value of each circRNA was assessed by receiver operating characteristic (ROC) curve. We identified 155 up-regulated circRNAs and 229 down-regulated ones by microarray analysis in PBMCs from CD patients compared with HCs. Besides, 4 circRNAs (092520, 102610, 004662, and 103124) were significantly up-regulated validated by RT-PCR and qPCR between CD and HCs. ROC curve analysis suggested important values of circRNAs (092520, 102610, 004662, and 103124) in CD diagnosis, with area under the curve (AUC) as 0.66, 0.78, 0.85, and 0.74, respectively. Then, we further identified that the relative expression levels of circRNA_004662 was upregulated significantly in CD patients compared with UC patients. Herein, the upregulation of the 4 circRNAs (092520, 102610, 004662, or 103124) in PBMCs can be served as potential diagnostic biomarkers of CD, and circRNA_004662 might be a novel candidate for differentiating CD from UC. Moreover, a circRNA-microRNA-mRNA network predicted that circRNA_004662 appeared to be correlated with mammalian target of rapamycin (mTOR) pathway.


Assuntos
Doença de Crohn/sangue , Leucócitos Mononucleares/metabolismo , RNA/sangue , Adolescente , Adulto , Idoso , Biomarcadores/sangue , Feminino , Humanos , Masculino , Análise em Microsséries , Pessoa de Meia-Idade , Curva ROC , Reação em Cadeia da Polimerase em Tempo Real , Transcriptoma , Adulto Jovem
11.
Medicine (Baltimore) ; 98(26): e16148, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31261542

RESUMO

Non-functioning pituitary adenomas (NFPAs) are the most common pituitary tumors, and some exhibit locally invasive or even clinically aggressive behavior. Circular RNAs (circRNAs) are a reinvented class of non-coding RNAs that play important roles in tumor initiation and progression.CircRNA microarray assays were performed in 4 invasive and 4 non-invasive NFPAs, and 4 typically differential expression circRNAs were selected for validation using quantitative reverse transcription-polymerase chain reaction. The diagnostic and prognostic values of tested cirRNAs were further evaluated. Bioinformatics analysis and a literature review of potential miRNAs targets involved in pituitary tumor invasion were performed.A specific circRNA expression profile was detected between invasive and non-invasive NFPAs, including 91 upregulated and 61 downregulated circRNAs in invasive tumors. The dysregulation of the 4 circRNAs has been confirmed. The expression of hsa_circRNA_102597, a downregulated circRNA, was significantly correlated with tumor diameter (P < .05) and Knosp grade (P < .01). Hsa_circRNA_102597 alone or in combined with Ki-67 index was able to accurately differentiate invasive from non-invasive NFPAs as well as predict tumor progression/recurrence. Fourteen aberrantly expressed circRNAs might be involved in the invasiveness of pituitary adenomas via seven predicted potential miRNA targets.CircRNAs are participated in pituitary tumor invasion, and may be used as novel diagnostic and prognostic biomarkers in NFPAs.


Assuntos
Adenoma/sangue , Invasividade Neoplásica/diagnóstico , Neoplasias Hipofisárias/sangue , RNA/sangue , Adolescente , Adulto , Idoso , Biomarcadores Tumorais/sangue , Biologia Computacional , Regulação para Baixo , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Masculino , Análise em Microsséries , Pessoa de Meia-Idade , Reação em Cadeia da Polimerase em Tempo Real
12.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 36(7): 676-681, 2019 Jul 10.
Artigo em Chinês | MEDLINE | ID: mdl-31302909

RESUMO

OBJECTIVE: To assess the value of chromosomal microarray analysis (CMA) and next-generation sequencing (NGS) for the analysis of abortic tissues. METHODS: A total of 242 samples of spontaneous abortion were collected and tested by CMA or NGS. RESULTS: The detection was successfully in 238 cases (98.35%). In total 143 cases of chromosomal abnormalities were detected, which accounted for 60.08% of all cases. Numerical chromosomal abnormalities were found in 133 cases(93.01%), structural abnormalities were found in 9 cases (6.29%), and uniparental disomy was found in 1 case(0.70%). CONCLUSION: Both CMA and NGS have the advantages of high-throughput, good coverage, high resolution and rapid analysis. They can be used for the detection of the causes of spontaneous abortions. CMA is more useful for the detection of aneuploidies and uniparental disomy, while NGS has advantages in its throughput, capacity in detecting low percentage chimerism and cost, which can provide more options for clinicians.


Assuntos
Aborto Espontâneo/genética , Aberrações Cromossômicas , Sequenciamento de Nucleotídeos em Larga Escala , Análise em Microsséries , Feminino , Humanos , Gravidez
13.
Malar J ; 18(1): 197, 2019 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-31196098

RESUMO

BACKGROUND: Vivax malaria is the predominant form of malaria outside Africa, affecting about 14 million people worldwide, with about 2.5 billion people exposed. Development of a Plasmodium vivax vaccine is a priority, and merozoite surface protein 7 (MSP-7) has been proposed as a plausible candidate. The P. vivax genome contains 12 MSP-7 genes, which contribute to erythrocyte invasion during blood-stage infection. Previous analysis of MSP-7 sequence diversity suggested that not all paralogs are functionally equivalent. To explore MSP-7 functional diversity, and to identify the best vaccine candidate within the family, MSP-7 expression and antigenicity during bloodstream infections were examined directly from clinical isolates. METHODS: Merozoite surface protein 7 gene expression was profiled using RNA-seq data from blood samples isolated from ten human patients with vivax malaria. Differential expression analysis and co-expression cluster analysis were used to relate PvMSP-7 expression to genetic markers of life cycle stage. Plasma from vivax malaria patients was also assayed using a custom peptide microarray to measure antibody responses against the coding regions of 12 MSP-7 paralogs. RESULTS: Ten patients presented diverse transcriptional profiles that comprised four patient groups. Two MSP-7 paralogs, 7A and 7F, were expressed abundantly in all patients, while other MSP-7 genes were uniformly rare (e.g. 7J). MSP-7H and 7I were significantly more abundant in patient group 4 only, (two patients having experienced longer patency), and were co-expressed with a schizont-stage marker, while negatively associated with liver-stage and gametocyte-stage markers. Screening infections with a PvMSP-7 peptide array identified 13 linear B-cell epitopes in five MSP-7 paralogs that were recognized by plasma from all patients. CONCLUSIONS: These results show that MSP-7 family members vary in expression profile during blood infections; MSP-7A and 7F are expressed throughout the intraerythrocytic development cycle, while expression of other paralogs is focused on the schizont. This may reflect developmental regulation, and potentially functional differentiation, within the gene family. The frequency of B-cell epitopes among paralogs also varies, with MSP-7A and 7L consistently the most immunogenic. Thus, MSP-7 paralogs cannot be assumed to have equal potential as vaccines. This analysis of clinical infections indicates that the most abundant and immunogenic paralog is MSP-7A.


Assuntos
Antígenos de Protozoários/biossíntese , Antígenos de Protozoários/imunologia , Vacinas Antimaláricas/imunologia , Malária Vivax/imunologia , Malária Vivax/prevenção & controle , Proteínas de Membrana/biossíntese , Proteínas de Membrana/imunologia , Proteínas de Protozoários/biossíntese , Proteínas de Protozoários/imunologia , Adolescente , Adulto , África , Idoso , Idoso de 80 Anos ou mais , Alelos , Anticorpos Antiprotozoários/sangue , Antígenos de Protozoários/genética , Criança , Pré-Escolar , Feminino , Perfilação da Expressão Gênica , Humanos , Lactente , Recém-Nascido , Masculino , Proteínas de Membrana/genética , Análise em Microsséries , Pessoa de Meia-Idade , Plasmodium vivax/imunologia , Proteínas de Protozoários/genética , Análise de Sequência de RNA , Adulto Jovem
14.
Int J Nanomedicine ; 14: 3297-3309, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31190794

RESUMO

Background: Cardiovascular disease (CVD) is the leading cause of mortality all over the world. Vascular stents are used to ameliorate vascular stenosis and recover vascular function. The application of nanotubular coatings has been confirmed to promote endothelial cell (EC) proliferation and function. However, the regulatory mechanisms involved in cellular responses to the nanotubular topography have not been defined. In the present study, a microarray analysis was performed to explore the expression patterns of long noncoding RNAs (lncRNAs) in human coronary artery endothelial cells (HCAECs) that were differentially expressed in response to nitinol-based nanotubular coatings. Materials and methods: First, anodization was performed to synthesize nitinol-based nanotubular coatings. Then, HCAECs were cultured on the samples for 24 h to evaluate cell cytoskeleton organization. Next, total RNA was extracted and synthesized into cRNA, which was hybridized onto the microarray. GO analysis and KEGG pathway analysis were performed to investigate the roles of differentially expressed messenger RNAs (mRNAs). Quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR) was performed to validate the expression of randomly selected lncRNAs. Coexpression networks were created to identify the interactions among lncRNAs and the protein-coding genes involved in nanotubular topography-induced biological and molecular pathways. Independent Student's t-test was applied for comparisons between two groups with statistical significance set at p<0.05. Results: 1085 lncRNAs and 227 mRNAs were significantly differentially expressed in the nitinol-based nanotubular coating group. Bioinformatics analysis revealed that extracellular matrix receptor interactions and cell adhesion molecules play critical roles in the sensing of nitinol-based nanotubular coatings by HCAECs. The TATA-binding protein (TBP) and TBP-associated transfactor 1 (TAF1) are important molecules in EC responses to substrate topography. Conclusion: This study suggests that nanotubular substrate topography regulates ECs by differentially expressed lncRNAs involved extracellular matrix receptor interactions and cell adhesion molecules.


Assuntos
Ligas/farmacologia , Materiais Revestidos Biocompatíveis/farmacologia , Vasos Coronários/citologia , Células Endoteliais/metabolismo , Regulação da Expressão Gênica/efeitos dos fármacos , Nanotubos/química , RNA Longo não Codificante/genética , Proliferação de Células/efeitos dos fármacos , Citoesqueleto/efeitos dos fármacos , Citoesqueleto/metabolismo , Células Endoteliais/efeitos dos fármacos , Perfilação da Expressão Gênica , Ontologia Genética , Redes Reguladoras de Genes/efeitos dos fármacos , Humanos , MicroRNAs/genética , MicroRNAs/metabolismo , Análise em Microsséries , Nanotubos/ultraestrutura , Fenótipo , RNA Longo não Codificante/metabolismo , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Reação em Cadeia da Polimerase em Tempo Real , Fatores de Transcrição/metabolismo
15.
Gene ; 706: 188-200, 2019 Jul 20.
Artigo em Inglês | MEDLINE | ID: mdl-31085273

RESUMO

Due to the rapid development of DNA microarray technology, a large number of microarray data come into being and classifying these data has been verified useful for cancer diagnosis, treatment and prevention. However, microarray data classification is still a challenging task since there are often a huge number of genes but a small number of samples in gene expression data. As a result, a computational method for reducing the dimension of microarray data is necessary. In this paper, we introduce a computational gene selection model for microarray data classification via adaptive hypergraph embedded dictionary learning (AHEDL). Specifically, a dictionary is learned from the feature space of original high dimensional microarray data, and this learned dictionary is used to represent original genes with a reconstruction coefficient matrix. Then we use a l2, 1-norm regularization to impose the row sparsity on the coefficient matrix for selecting discriminate genes. Meanwhile, in order to capture the localmanifold geometrical structure of original microarray data in a high-order manner, a hypergraph is adaptively learned and embedded into the model. An iterative updating algorithm is designed for solving the optimization problem. In order to validate the efficacy of the proposed model, we have conducted experiments on six publicly available microarray data sets and the results demonstrate that AHEDL outperforms other state-of-the-art methods in terms of microarray data classification. ABBREVIATIONS.


Assuntos
Biologia Computacional/métodos , Análise em Microsséries/métodos , Algoritmos , Big Data , Biologia Computacional/estatística & dados numéricos , Análise de Dados , Humanos , Análise em Microsséries/estatística & dados numéricos
16.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 36(6): 571-573, 2019 Jun 10.
Artigo em Chinês | MEDLINE | ID: mdl-31055807

RESUMO

OBJECTIVE: To carry out prenatal diagnosis for two cases of Pallister-Killian syndrome (PKS) using combined chromosomal microarray analysis (CMA) and fluorescence in situ hybridization (FISH). METHODS: Umbilical cord blood was sampled from the two fetuses and subjected to G-banding chromosomal karyotyping, CMA and FISH assay. RESULTS: Chromosomal karyotyping showed that the two fetuses were mos 47,XX,+i(12)(p10)[3]/46,XX[197] and mos 47,XY,+i(12)(p10)[5]/46,XY[95], respectively. CMA showed that both had carried duplication of 12p. The results of interphase FISH confirmed mosaicism of 12p tetrasomy. Combined with ultrasonographic findings, both fetuses were diagnosed as PKS. CONCLUSION: Prenatal ultrasound examination, karyotype analysis of umbilical cord blood, G-banded chromosomal analysis, CMA and FISH may be used in conjunct for the prenatal diagnosis of PKS.


Assuntos
Transtornos Cromossômicos , Transtornos Cromossômicos/diagnóstico , Cromossomos Humanos Par 12 , Feminino , Humanos , Hibridização in Situ Fluorescente , Análise em Microsséries , Mosaicismo , Gravidez , Diagnóstico Pré-Natal
17.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 36(6): 613-615, 2019 Jun 10.
Artigo em Chinês | MEDLINE | ID: mdl-31055819

RESUMO

OBJECTIVE: To explore the genetic etiology for a child with ocular dysplasia. METHODS: Clinical examination was carried out. Medical history of the child was collected. Genomic DNA was extracted from peripheral blood samples. Chromosomal microarray analysis (CMA) was used to detect potential genomic copy number variations. RESULTS: Ultrasonography revealed cataracts in both eyes of the child. MRI showed increased extracranial space, supratentorial ventricular dilatation, reduced white matter volume, increased T2WI signal and a large occipital cisterna. CMA showed that the patient carried a 249 kb microdeletion at Xq25q26.1 region, namely [hg19]arrXq25q26.1 (128 652 372 - 128 901 629)×0. CONCLUSION: The child was diagnosed with Lowe syndrome, for which the 249 kb microdeletion at Xq25q26.1 is probably accountable.


Assuntos
Síndrome Oculocerebrorrenal , Criança , Aberrações Cromossômicas , Variações do Número de Cópias de DNA , Humanos , Análise em Microsséries
18.
Medicine (Baltimore) ; 98(21): e15796, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31124977

RESUMO

miRNAs and genes play significant roles in the etiology and pathogenesis of intervertebral disc degeneration (IDD). This study aimed to identify aberrantly expressed miRNAs, genes, and pathways in IDD through a comprehensive bioinformatics analysis.Data of miRNAs expression microarrays (GSE63492) and genes microarrays (GSE23130) were obtained from GEO database. Similarly, aberrantly expressed miRNAs and genes were obtained using GEO2R. In addition, functional and enrichment analyses of selected miRNAs and genes were performed using the DAVID database. Meanwhile, protein-protein interaction (PPI) network was constructed using STRING, and then visualized in Cytoscape.A total of 98 upregulated miRNAs were identified. They were enriched in biological processes of response to organelle, ion binding, cellular nitrogen compound metabolic process, biosynthetic process, small molecule metabolic process, cellular protein modification process, catabolic process, molecular function, neurotrophin TRK receptor signaling pathway, and protein complex. In addition, 1405 high expression protein genes were detected. It indicated enrichment in biological processes, such as translational initiation, nonsense-mediated decay, viral transcription, cell-cell adhesion, rRNA processing, translation, RP-dependent cotranslational protein targeting to membrane, nuclear-transcribed mRNA catabolic process, regulation of mRNA stability, and mRNA splicing via spliceosome and extracellular matrix organization. In addition, pathway analysis exhibited the common enrichment in focal adhesion, Hippo signaling pathway, ECM-receptor interaction, Wnt signaling pathway, PI3K-Akt signaling pathway, endocytosis, proteoglycans in cancer, and so on. The top 10 central genes of PPI network were POTEE, PPP2CA, RPL17, HSP90AA1, POTEF, RPL13A, ACTB, RPL18, RPS24, and HSPA1A.In conclusion, our research proposed abnormally expressed miRNAs, genes, and pathways in IDD through bioinformatics methods, which may provide new insights into the pathogenesis of IDD. Thus, the Hub gene involving POTEE, PPP2CA, RPL17, HSP90AA1, POTEF, RPL13A, ACTB, RPL18, RPS24, and HSPA1A may be biomarkers for accurate diagnosis and treatment of IDD in the future.


Assuntos
Mineração de Dados/métodos , Degeneração do Disco Intervertebral/genética , MicroRNAs/genética , Transdução de Sinais/genética , Revisão Sistemática como Assunto , Biologia Computacional/métodos , Ontologia Genética , Marcadores Genéticos/genética , Humanos , Análise em Microsséries , Mapas de Interação de Proteínas , Projetos de Pesquisa
19.
Vet Microbiol ; 233: 196-203, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31053353

RESUMO

In recent years an increasing number of methicillin-resistant S. pseudintermedius (MRSP) has been observed in both, healthy and clinically infected dogs. The aim of the study was the characterisation of MRSP isolates from clinical routine diagnostics of a German laboratory in order to assess the abundancy of resistance genes and SCCmec elements. 97 isolates from 96 dogs were analysed using microarrays detecting resistance genes and SCCmec-associated markers. All isolates harboured mecA and blaZ. Other abundant resistance markers (in >80% of isolates) included aacA-aphD, aphA3 and sat as well as erm(B). Tetracycline resistance genes (tet(K), tet(M)) and cat also were common (in >20%). The vast majority (n = 59) of isolates carried SCCmec III elements. SCCmec IV and V elements were identified in 21 and 15 isolates, respectively. Irregular or pseudo-SCCmec elements were found in 2 isolates. The high degree of uniformity of hybridisation patterns of tested strains suggest that the majority of MRSP infections was caused by one single strain and comparison to previously published reports and sequences suggest that this was the ST71-SCCmec III strain that also predominates elsewhere in Western Europe.


Assuntos
Farmacorresistência Bacteriana Múltipla/genética , Variação Genética , Resistência a Meticilina/genética , Infecções Estafilocócicas/veterinária , Staphylococcus/classificação , Animais , Técnicas de Tipagem Bacteriana , Doenças do Cão/microbiologia , Cães , Meticilina/farmacologia , Análise em Microsséries , Tipagem de Sequências Multilocus , Infecções Estafilocócicas/microbiologia , Staphylococcus/efeitos dos fármacos
20.
Bull Exp Biol Med ; 166(6): 788-792, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31028584

RESUMO

The effect of low concentrations of miRNA on the ability of GeneChip miRNA 4.0 hybridization chips to evaluate their representation in the sample was studied. It is shown that the evaluation of the expression of 61 miRNAs is statistically significantly associated with the multiplicity of plasma dilution. Only 12 miRNAs showed very high Pearson correlation coefficient (>0.95) and they all decreased in response to dilution. High abundance of has-miR-4532 miRNA in plasma was demonstrated. This miRNA was never detected during sequencing of similar samples. It was concluded that in case of miRNA expression <1.12±0.33 units in log2 scale, dilution was not followed by further decrease in the signal intensity in GeneChip miRNA 4.0 chips.


Assuntos
MicroRNAs/sangue , Análise em Microsséries/métodos , Manejo de Espécimes/métodos , Humanos , MicroRNAs/genética , Hibridização de Ácido Nucleico/métodos , Sensibilidade e Especificidade
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