RESUMO
The objective of this paper was to identify hub genes and pathways associated with retinoblastoma using centrality analysis of the co-expression network and pathway-enrichment analysis. The co-expression network of retinoblastoma was constructed by weighted gene co-expression network analysis (WGCNA) based on differentially expressed (DE) genes, and clusters were obtained through the molecular complex detection (MCODE) algorithm. Degree centrality analysis of the co-expression network was performed to explore hub genes present in retinoblastoma. Pathway-enrichment analysis was performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Validation of hub gene expression in retinoblastoma was performed by reverse transcription-polymerase chain reaction (RT-PCR) analysis. The co-expression network based on 221 DE genes between retinoblastoma and normal controls consisted of 210 nodes and 3965 edges, and 5 clusters of the network were evaluated. By assessing the centrality analysis of the co-expression network, 21 hub genes were identified, such as SNORD115-41, RASSF2, and SNORD115-44. According to RT-PCR analysis, 16 of the 21 hub genes were differently expressed, including RASSF2 and CDCA7, and 5 were not differently expressed in retinoblastoma compared to normal controls. Pathway analysis showed that genes in 2 clusters were enriched in 3 pathways: purine metabolism, p53 signaling pathway, and melanogenesis. In this study, we successfully identified 16 hub genes and 3 pathways associated with retinoblastoma, which may be potential biomarkers for early detection and therapy for retinoblastoma.
Assuntos
Regulação Neoplásica da Expressão Gênica , Redes Reguladoras de Genes , Mapas de Interação de Proteínas , Retinoblastoma/genética , Retinoblastoma/metabolismo , Transdução de Sinais , Algoritmos , Biologia Computacional/métodos , Bases de Dados Genéticas , Perfilação da Expressão Gênica , Humanos , Reprodutibilidade dos TestesRESUMO
Gibberellins (GA) are some of the most important phytohormones involved in plant development. DELLA proteins are negative regulators of GA signaling in many plants. In this study, the full-length cDNA sequences of three DELLA genes were cloned from Artemisia annua. Phylogenetic analysis revealed that AaDELLA1 and AaDELLA2 were located in the same cluster, but AaDELLA3 was not. Subcellular localization analysis suggested that AaDELLAs can be targeted to the nucleus and/or cytoplasm. Real-time PCR indicated that all three AaDELLA genes exhibited the highest expression in seeds. Expression of all AaDELLA genes was enhanced by exogenous MeJA treatment but inhibited by GA3 treatment. Yeast two-hybrid assay showed that AaDELLAs could interact with basic helix-loop-helix transcription factor AaMYC2, suggesting that GA and JA signaling may be involved in cross-talk via DELLA and MYC2 interaction in A. annua.
Assuntos
Artemisia annua/genética , Clonagem Molecular , Expressão Gênica , Proteínas de Plantas/genética , Sequência de Aminoácidos , Artemisia annua/classificação , Artemisia annua/metabolismo , Biologia Computacional/métodos , DNA Complementar/química , DNA Complementar/genética , Evolução Molecular , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Modelos Moleculares , Dados de Sequência Molecular , Filogenia , Reguladores de Crescimento de Plantas/farmacologia , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Ligação Proteica , Conformação Proteica , Transporte Proteico , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Alinhamento de SequênciaRESUMO
Numerous studies have evaluated the association between the MTHFR A1298C polymorphism and ovarian cancer risk. However, the specific association is still controversial. Therefore, we performed the present meta-analysis. A systematic literature search of PubMed and Embase databases was undertaken in August 2014, and the reference lists of articles were retrieved. ORs with their 95%CI were calculated to evaluate the strength of the association. Meta-analysis was performed using the STATA version 12.0 software package and publication bias was investigated by Begg's funnel plot. Five case-control studies from three publications (with 7026 subjects) on the relationship between the MTHFR A1298C polymorphism and ovarian cancer were analyzed by meta-analysis. Overall, no significant variation in ovarian cancer risk was detected in any of the genetic models (AA vs CC: OR = 0.93, 95%CI = 0.78-1.10; AA vs AC: OR = 1.02, 95%CI = 0.92-1.13; dominant model: OR = 1.00, 95%CI = 0.91-1.10; recessive model: OR = 0.92, 95%CI = 0.78-1.08). In conclusion, this meta-analysis suggests that the A1298C polymorphism in the MTHFR gene may be not associated with susceptibility to ovarian cancer.
Assuntos
Predisposição Genética para Doença , Metilenotetra-Hidrofolato Redutase (NADPH2)/genética , Neoplasias Ovarianas/enzimologia , Neoplasias Ovarianas/genética , Polimorfismo de Nucleotídeo Único/genética , Intervalos de Confiança , Feminino , Humanos , Razão de Chances , Viés de Publicação , Fatores de RiscoRESUMO
BACKGROUND: MicroRNAs (miRNAs) in body fluids such as serum and plasma can be stably detected and used as potential biomarkers in hepatocellular carcinoma (HCC) diagnosis. OBJECTIVE: To systematically evaluate circulating miRNAs from HCC expression profiling studies and to determine miRNA biomarkers for HCC detection. METHODS: A systematic review and meta-analysis of published studies were carried out for comparing the circulating miRNA expressions between HCC patients and healthy people, hepatitis, or cirrhosis patients. A miRNA ranking system that considered the number of comparisons in agreement and total number of samples was used. Then the summary receiver-operating characteristic curve (sROC) results of the top miRNAs were combined to further evaluate their diagnostic value using Meta-disc 1.4. RESULTS: In the 17 included studies, three circulating miRNAs (miR-21, miR-122, and miR-223) were repeatedly reported three times or more in both HCC patients vs. healthy controls and vs. other hepatitis or cirrhosis patients. In further analysis, the area under curve (AUC) of sROC for miR-21, miR-122 and miR-223 in discriminating HCC patients from healthy people are 0.9293, 0.8128, and 0.8597, respectively. CONCLUSIONS: Circulating miR-21 has highest level of diagnostic efficiency among three miRNAs candidate biomarkers (miR-21, miR-122, and miR-223) for detection of HCC.
Assuntos
Biomarcadores Tumorais/genética , Carcinoma Hepatocelular/diagnóstico , Neoplasias Hepáticas/diagnóstico , MicroRNAs/genética , Biomarcadores Tumorais/sangue , Carcinoma Hepatocelular/sangue , Carcinoma Hepatocelular/genética , Humanos , Neoplasias Hepáticas/sangue , Neoplasias Hepáticas/genética , MicroRNAs/sangueRESUMO
Finding an efficient and affordable treatment against malaria is still a challenge for medicine. Artemisinin is an effective anti-malarial drug isolated from Artemisia annua. However, the artemisinin content of A. annua is very low. We used transgenic technology to increase the artemisinin content of A. annua by overexpressing cytochrome P450 monooxygenase (cyp71av1) and cytochrome P450 reductase (cpr) genes. CYP71AV1 is a key enzyme in the artemisinin biosynthesis pathway, while CPR is a redox partner for CYP71AV1. Eight independent transgenic A. annua plants were obtained through Agrobacterium tumefaciens-mediated transformation, which was confirmed by PCR and Southern blot analyses. The real-time qPCR results showed that the gene cyp71av1 was highly expressed at the transcriptional level in the transgenic A. annua plants. HPLC analysis showed that the artemisinin content was increased in a number of the transgenic plants, in which both cyp71av1 and cpr were overexpressed. In one of the transgenic A. annua plants, the artemisinin content was 38% higher than in the non-transgenic plants. We conclude that overexpressing key enzymes of the biosynthesis pathway is an effective means for increasing artemisinin content in plants.