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Microarray Analysis of chemosensitivity in Hypopharyngeal Squamous Cell Carcinoma

ABSTRACT: OBJECTIVE: To investigate the differentially expressed genes and miRNAs related to the chemosensitivity of hypopharyngeal squamous cell carcinoma （HSCC）by microarrays and miRNA arrays. METHODS: 1. A total number of 21 patients who underwent induction chemotherapy for primary hypopharyngeal squamous cell carcinoma (12 patients are sensitive to chemotherapy ,and others are not) were recruited for microarray and miRNA array gene expression analysis 2. Bioinformatics analysis of differentially expressed genes screened by microarrays : The differential gene cluster analysis was applied in biological processes, cellular components and molecular functions by GO database; The differential gene enrichment analysis was applied in signaling pathways by KEGG database, and the differentially expressed and biologically meaningful core genes would be screened. 3. Prediction and analysis of target genes of differentially expressed miRNAs: TargetScan, PITA and microRNAorg methods were used for target gene prediction in GeneSpring 12.5 software, and the intersection of the three methods analysis was considered as significant target genes. Considering the result of microarrays, the intersection of the predicted target genes and the genes screened by microarrays would be analyzed by bioinformatics, which were considered as genes regulated by different miRNAs. RESULTS: 1. Analyzed by microarrays, there were 1579 genes significantly related to the sensitivity to chemotherapy; Among these 1579genes, 815 showed a higher expression in the tissue from patients who are sensitive to chemotherapy , while 764 presented the contrasting pattern. 2. Analyzed by miRNA arrays, there were 24 genes significantly related to the sensitivity to chemotherapy; Among them, 6 showed a higher expression in the tissue from patients who are sensitive to chemotherapy , while 18 presented the contrasting pattern. TargetScan, PITA and microRNAorg were used for target gene prediction in GeneSpring 12.5 software, and the intersection of the three methods analysis was considered as significant target genes. There were 613 putative target genes corresponding to the 24 significant miRNAs. Among them, six genes(MAPK14, ADCY1, GSTM4, CDC42, JUN, GPX6) were statistically and biologically different related to the sensitivity to chemotherapy. And among the 24 significant miRNAs, miR-193b-3p、miR-211-3p、miR-4253、miR-4496、miR-6738-5p could regulate them. CONCLUSIONS: The research revealed a gene expression signature of chemosensitivity in hypopharyngeal squamous cell carcinoma by microarrays and miRNA arrays. The result will contribute to the understanding of the molecular basis of hypopharyngeal squamous cell carcinoma and help to improve diagnosis and treatment.

ORGANISM(S): synthetic construct Homo sapiens

PROVIDER: GSE85608 | GEO | 2016/08/16

SECONDARY ACCESSION(S): PRJNA338945

REPOSITORIES: GEO

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Project description:OBJECTIVE: To investigate the differentially expressed genes and miRNAs related to the chemosensitivity of hypopharyngeal squamous cell carcinoma ï¼HSCCï¼by microarrays and miRNA arrays. METHODS: 1. A total number of 21 patients who underwent induction chemotherapy for primary hypopharyngeal squamous cell carcinoma (12 patients are sensitive to chemotherapy ,and others are not) were recruited for microarray and miRNA array gene expression analysis 2. Bioinformatics analysis of differentially expressed genes screened by microarrays : The differential gene cluster analysis was applied in biological processes, cellular components and molecular functions by GO database; The differential gene enrichment analysis was applied in signaling pathways by KEGG database, and the differentially expressed and biologically meaningful core genes would be screened. 3. Prediction and analysis of target genes of differentially expressed miRNAs: TargetScan, PITA and microRNAorg methods were used for target gene prediction in GeneSpring 12.5 software, and the intersection of the three methods analysis was considered as significant target genes. Considering the result of microarrays, the intersection of the predicted target genes and the genes screened by microarrays would be analyzed by bioinformatics, which were considered as genes regulated by different miRNAs. RESULTS: 1. Analyzed by microarrays, there were 1579 genes significantly related to the sensitivity to chemotherapy; Among these 1579genes, 815 showed a higher expression in the tissue from patients who are sensitive to chemotherapy , while 764 presented the contrasting pattern. 2. Analyzed by miRNA arrays, there were 24 genes significantly related to the sensitivity to chemotherapy; Among them, 6 showed a higher expression in the tissue from patients who are sensitive to chemotherapy , while 18 presented the contrasting pattern. TargetScan, PITA and microRNAorg were used for target gene prediction in GeneSpring 12.5 software, and the intersection of the three methods analysis was considered as significant target genes. There were 613 putative target genes corresponding to the 24 significant miRNAs. Among them, six genes(MAPK14, ADCY1, GSTM4, CDC42, JUN, GPX6) were statistically and biologically different related to the sensitivity to chemotherapy. And among the 24 significant miRNAs, miR-193b-3pãmiR-211-3pãmiR-4253ãmiR-4496ãmiR-6738-5p could regulate them. CONCLUSIONS: The research revealed a gene expression signature of chemosensitivity in hypopharyngeal squamous cell carcinoma by microarrays and miRNA arrays. The result will contribute to the understanding of the molecular basis of hypopharyngeal squamous cell carcinoma and help to improve diagnosis and treatment. 1. A total number of 21 patients who underwent induction chemotherapy for primary hypopharyngeal squamous cell carcinoma (12 patients are sensitive to chemotherapy ,and others are not) were recruited for microarray and miRNA array gene expression analysis 2. Bioinformatics analysis of differentially expressed genes screened by microarrays : The differential gene cluster analysis was applied in biological processes, cellular components and molecular functions by GO database; The differential gene enrichment analysis was applied in signaling pathways by KEGG database, and the differentially expressed and biologically meaningful core genes would be screened. 3. Prediction and analysis of target genes of differentially expressed miRNAs: TargetScan, PITA and microRNAorg methods were used for target gene prediction in GeneSpring 12.5 software, and the intersection of the three methods analysis was considered as significant target genes. Considering the result of microarrays, the intersection of the predicted target genes and the genes screened by microarrays would be analyzed by bioinformatics, which were considered as genes regulated by different miRNAs.

Project description:Objective: The purpose of this study was to investigate the miRNAs basis of tumorigenesis in LSCC, and analyze the physiological processes of target genes predicted by the screened miRNAs that may be useful for the effective therapeutic strategies. Methods: A total number of 6 patients who underwent surgery for primary laryngeal squamous cell carcinoma were recruited for miRNA array analysis. LSCC tissues compared with corresponding adjacent non-neoplastic tissues were analysed by the Affymetrix GeneChip miRNA Array 3.0 to screen effective miRNAs, then TargetScan,PITA and microRNAorg were used for target gene prediction in GeneSpring 12.5 software.Moreover, pathway-based methods were adopted to analyse physiological processes of the target genes. The screened miRNAs and the significant target genes were also validated by qRT-PCR in another 36 patients diagnosed for LSCC. Results: Analysed by the miRNAs arrays, there were seven miRNAs (hsa-miR-224, hsa-miR-183, hsa-miR-23a, hsa-miR-675, hsa-miR-27a, hsa-miR-503 and hsa-miR-4800-3p) significantly related to tumorigenesis ,and all the screened miRNAs in laryngeal squamous cell carcinoma tissues were significantly up-regulated(P<0.05). The expressions of these miRNAs were also validated by qRT-PCR. Then analysed by GeneSpring 12.5 software, there were 72 putative target genes corresponding to the seven significant miRNAs. Moreover,analysed by String database,the result indicated that most target genes could be composed of gene networks; Analysed by GO database, we observed that these target genes were involved in processes such as metabolic process, biological regulation,membrane,protein binding,ion binding and so on (P <0.05); Analysed by KEGG pathways database, MAPK signaling pathway, adherens junction and pathways in cancer played especially important role in tumorigenesis of LSCC (P<0.05). As the two important genes in MAPK signaling pathway which plays pivotal roles in tumorigenesis, FGF2 and MAP2K4 were validated by qRT-PCR, and they were significantly down-regulated(P<0.05). Conclusions: The research revealed seven miRNAs expression signature(hsa-miR-224, hsa-miR-183, hsa-miR-23a, hsa-miR-675, hsa-miR-27a, hsa-miR-503 and hsa-miR-4800-3p) of tumorigenesis in laryngeal squamous cell carcinoma,and analysed the physiological processes of the predicted target genes regulated by screened miRNAs in LSCC. The result will contribute to the understanding of the molecular basis of LSCC and help to improve the treatment. A total number of 6 patients who underwent surgery for primary laryngeal squamous cell carcinoma were recruited for miRNA array analysis. LSCC tissues compared with corresponding adjacent non-neoplastic tissues were analysed by the Affymetrix GeneChip miRNA Array 3.0 to screen effective miRNAs, then TargetScan,PITA and microRNAorg were used for target gene prediction in GeneSpring 12.5 software.Moreover, pathway-based methods were adopted to analyse physiological processes of the target genes. The screened miRNAs and the significant target genes were also validated by qRT-PCR in another 36 patients diagnosed for LSCC.

Project description:OBJECTIVE: To investigate the differentially expressed genes related to the chemosensitivity of laryngeal squamous cell carcinoma ï¼LSCCï¼by microarrays arrays. METHODS: 1. A total number of 11 patients who underwent induction chemotherapy for primary hypopharyngeal squamous cell carcinoma (7 patients are sensitive to chemotherapy ,and others are not) were recruited for microarray and miRNA array gene expression analysis 2. Bioinformatics analysis of differentially expressed genes screened by microarrays : The differential gene cluster analysis was applied in biological processes, cellular components and molecular functions by GO database; The differential gene enrichment analysis was applied in signaling pathways by KEGG database, and the differentially expressed and biologically meaningful core genes would be screened. RESULTS: 1. Analyzed by microarrays, there were 1554 genes significantly related to the sensitivity to chemotherapy; Among these 1554genes, 777 showed a higher expression in the tissue from patients who are sensitive to chemotherapy , while 785 presented the contrasting pattern. CONCLUSIONS: The research revealed a gene expression signature of chemosensitivity in laryngeal squamous cell carcinoma by microarrays arrays. The result will contribute to the understanding of the molecular basis of laryngeal squamous cell carcinoma and help to improve diagnosis and treatment. 1. A total number of 11 patients who underwent induction chemotherapy for primary hypopharyngeal squamous cell carcinoma (7 patients are sensitive to chemotherapy ,and others are not) were recruited for microarray and miRNA array gene expression analysis 2. Bioinformatics analysis of differentially expressed genes screened by microarrays : The differential gene cluster analysis was applied in biological processes, cellular components and molecular functions by GO database; The differential gene enrichment analysis was applied in signaling pathways by KEGG database, and the differentially expressed and biologically meaningful core genes would be screened.

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Microarray Analysis of chemosensitivity in Hypopharyngeal Squamous Cell Carcinoma

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