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Gene microarray analysis of lncRNA and mRNA expression profiles in patients with hypopharyngeal squamous cell carcinoma.

ABSTRACT: BACKGROUND:Studies have shown that long noncoding RNAs (lncRNAs) are involved in the development and progression of many types of cancer. However, the mechanisms by which lncRNAs influence development and progression of hypopharyngeal squamous cell carcinoma (HSCC) are unclear. METHOD:We investigated differences in lncRNA and mRNA expression profiles between 3 pairs of HSCC tissues and adjacent nontumor tissues by microarray analysis. RESULTS:In HSCC tissues, 1299 lncRNAs were significantly upregulated (n=669) or downregulated (n=630) compared to levels in adjacent nontumor tissues. Moreover, 1432 mRNAs were significantly upregulated (n=684) or downregulated (n=748) in HSCC tissues. We randomly selected 2 differentially expressed lncRNAs (AB209630, AB019562) and 2 differentially expressed mRNAs (SPP1, TJP2) for confirmation of microarray results using qRT-PCR. The qRT-PCR results matched well with the microarray data. The differentially expressed lncRNAs and mRNAs were distributed on each of the chromosomes, including the X and Y chromosomes. Pathway analysis indicated that the biological functions of differentially expressed mRNAs were related to 48 cellular pathways that may be associated with HSCC development. GO analysis revealed that 593 mRNAs involved in biological processes, 50 mRNAs involved in cellular components, and 46 mRNAs involved in molecular functions were upregulated in the carcinomas; 280 mRNAs involved in biological processes, 58 mRNAs involved in cellular components, and 71 mRNAs involved in molecular functions were downregulated in the carcinomas. In addition, 8 enhancer-like lncRNAs and 21 intergenic lncRNAs with their adjacent mRNA pairs were identified as coregulated transcripts. CONCLUSION:These findings provide insight into the mechanisms underlying HSCC tumorigenesis and will facilitate identification of new therapeutic targets and diagnostic biomarkers for this disease.

SUBMITTER: Zhou J

PROVIDER: S-EPMC4483811 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Gene microarray analysis of lncRNA and mRNA expression profiles in patients with hypopharyngeal squamous cell carcinoma.

Zhou Jieyu J Li Wenming W Jin Tong T Xiang Xuan X Li Maocai M Wang Juan J Li Guojun G Pan Xinliang X Lei Dapeng D

International journal of clinical and experimental medicine 20150415 4

<h4>Background</h4>Studies have shown that long noncoding RNAs (lncRNAs) are involved in the development and progression of many types of cancer. However, the mechanisms by which lncRNAs influence development and progression of hypopharyngeal squamous cell carcinoma (HSCC) are unclear.<h4>Method</h4>We investigated differences in lncRNA and mRNA expression profiles between 3 pairs of HSCC tissues and adjacent nontumor tissues by microarray analysis.<h4>Results</h4>In HSCC tissues, 1299 lncRNAs w ...[more]

PMID: 26131061

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Project description: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.

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.

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Gene microarray analysis of lncRNA and mRNA expression profiles in patients with hypopharyngeal squamous cell carcinoma.

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Gene microarray analysis of lncRNA and mRNA expression profiles in patients with hypopharyngeal squamous cell carcinoma.

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