Analysis of cyclin E co-expression genes reveals nuclear transcription factor Y subunit alpha is an oncogene in gastric cancer

Objective: To explore genes potentially co-expressed with cyclin E in gastric cancer and discover possible targets for gastric cancer treatment. Methods: The Cancer Genome Atlas (TCGA) stomach adenocarcinoma sequencing data were used to predict genes co-expressed with cyclin E. Co-expression genes p...

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Autores principales: Liang-Yu Bie, Dan Li, Yu Mu, Sheng Wang, Bei-Bei Chen, Hui-Fang Lyu, Li-Li Han, Cai-Yun Nie, Chang-Cheng Yang, Lin Wang, Chuan-Chuan Ren, Wei-Jie Zhang, Ping Guo, Feng Shi, Qing-Xia Fan, Liu-Xing Wang, Xiao-Bing Chen, Su-Xia Luo
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Publicado: KeAi Communications Co., Ltd. 2019
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spelling oai:doaj.org-article:35e896724d9748c68bcfb80d859297132021-12-02T17:30:54ZAnalysis of cyclin E co-expression genes reveals nuclear transcription factor Y subunit alpha is an oncogene in gastric cancer2095-882X10.1016/j.cdtm.2018.07.003https://doaj.org/article/35e896724d9748c68bcfb80d859297132019-03-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2095882X17301068https://doaj.org/toc/2095-882XObjective: To explore genes potentially co-expressed with cyclin E in gastric cancer and discover possible targets for gastric cancer treatment. Methods: The Cancer Genome Atlas (TCGA) stomach adenocarcinoma sequencing data were used to predict genes co-expressed with cyclin E. Co-expression genes predicted by cBioPortal online analysis with Pearson correlation coefficient ≥0.4 were analyzed by gene ontology (GO) enrichment annotation using the PANTHER online platform (Ver. 7). Interactions between proteins encoded by these genes were analyzed using the STRING online platform (Ver. 10.5) and Cytoscape software (Ver. 3.5.1). Genes displaying a high degree of connection were analyzed by transcription factor enrichment prediction using FunRich software (Ver. 3). The significant transcription factor and cyclin E expression levels and their impact on gastric cancer progression were analyzed by Western blotting and Kaplan–Meier survival curve analysis. Results: After filtering the co-expression gene prediction results, 78 predicted genes that included 73 protein coding genes and 5 non-coding genes with Pearson correlation coefficient ≥0.4 were selected. The expressions of the genes were considered to be correlated with cyclin E expression. Among the 78 genes co-expressed with cyclin E, 19 genes at the central of the regulatory network associated with cyclin E were discovered. Nuclear transcription factor Y subunit alpha (NF-YA) was identified as a significant transcription factor associated with cyclin E co-expressing genes. Analysis of specimen donors’ clinical records revealed that high expression of NF-YA tended to be associated with increased cyclin E expression. The expression of both was associated with progression of gastric cancer. Western blotting results showed that compared with normal tissues, NF-YA and cyclin E were highly expressed in tumor tissues (P < 0.001). Survival curve analysis clearly demonstrated relatively poor overall survival of gastric cancer patients with high cyclin E or high NF-YA expression level, compared to patients with low cyclin E or NF-YA expression (P < 0.05). Conclusions: NF-YA may promote gastric cancer progression by increasing the transcription of cyclin E and other cell cycle regulatory genes. NF-YA might be a potential therapeutically useful prognostic factor for gastric cancer. Keywords: Cyclin E, Nuclear transcription factor Y subunit alpha, Oncogene, Gastric cancerLiang-Yu BieDan LiYu MuSheng WangBei-Bei ChenHui-Fang LyuLi-Li HanCai-Yun NieChang-Cheng YangLin WangChuan-Chuan RenWei-Jie ZhangPing GuoFeng ShiQing-Xia FanLiu-Xing WangXiao-Bing ChenSu-Xia LuoKeAi Communications Co., Ltd.articleMedicine (General)R5-920ENChronic Diseases and Translational Medicine, Vol 5, Iss 1, Pp 44-52 (2019)
institution DOAJ
collection DOAJ
language EN
topic Medicine (General)
R5-920
spellingShingle Medicine (General)
R5-920
Liang-Yu Bie
Dan Li
Yu Mu
Sheng Wang
Bei-Bei Chen
Hui-Fang Lyu
Li-Li Han
Cai-Yun Nie
Chang-Cheng Yang
Lin Wang
Chuan-Chuan Ren
Wei-Jie Zhang
Ping Guo
Feng Shi
Qing-Xia Fan
Liu-Xing Wang
Xiao-Bing Chen
Su-Xia Luo
Analysis of cyclin E co-expression genes reveals nuclear transcription factor Y subunit alpha is an oncogene in gastric cancer
description Objective: To explore genes potentially co-expressed with cyclin E in gastric cancer and discover possible targets for gastric cancer treatment. Methods: The Cancer Genome Atlas (TCGA) stomach adenocarcinoma sequencing data were used to predict genes co-expressed with cyclin E. Co-expression genes predicted by cBioPortal online analysis with Pearson correlation coefficient ≥0.4 were analyzed by gene ontology (GO) enrichment annotation using the PANTHER online platform (Ver. 7). Interactions between proteins encoded by these genes were analyzed using the STRING online platform (Ver. 10.5) and Cytoscape software (Ver. 3.5.1). Genes displaying a high degree of connection were analyzed by transcription factor enrichment prediction using FunRich software (Ver. 3). The significant transcription factor and cyclin E expression levels and their impact on gastric cancer progression were analyzed by Western blotting and Kaplan–Meier survival curve analysis. Results: After filtering the co-expression gene prediction results, 78 predicted genes that included 73 protein coding genes and 5 non-coding genes with Pearson correlation coefficient ≥0.4 were selected. The expressions of the genes were considered to be correlated with cyclin E expression. Among the 78 genes co-expressed with cyclin E, 19 genes at the central of the regulatory network associated with cyclin E were discovered. Nuclear transcription factor Y subunit alpha (NF-YA) was identified as a significant transcription factor associated with cyclin E co-expressing genes. Analysis of specimen donors’ clinical records revealed that high expression of NF-YA tended to be associated with increased cyclin E expression. The expression of both was associated with progression of gastric cancer. Western blotting results showed that compared with normal tissues, NF-YA and cyclin E were highly expressed in tumor tissues (P < 0.001). Survival curve analysis clearly demonstrated relatively poor overall survival of gastric cancer patients with high cyclin E or high NF-YA expression level, compared to patients with low cyclin E or NF-YA expression (P < 0.05). Conclusions: NF-YA may promote gastric cancer progression by increasing the transcription of cyclin E and other cell cycle regulatory genes. NF-YA might be a potential therapeutically useful prognostic factor for gastric cancer. Keywords: Cyclin E, Nuclear transcription factor Y subunit alpha, Oncogene, Gastric cancer
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author Liang-Yu Bie
Dan Li
Yu Mu
Sheng Wang
Bei-Bei Chen
Hui-Fang Lyu
Li-Li Han
Cai-Yun Nie
Chang-Cheng Yang
Lin Wang
Chuan-Chuan Ren
Wei-Jie Zhang
Ping Guo
Feng Shi
Qing-Xia Fan
Liu-Xing Wang
Xiao-Bing Chen
Su-Xia Luo
author_facet Liang-Yu Bie
Dan Li
Yu Mu
Sheng Wang
Bei-Bei Chen
Hui-Fang Lyu
Li-Li Han
Cai-Yun Nie
Chang-Cheng Yang
Lin Wang
Chuan-Chuan Ren
Wei-Jie Zhang
Ping Guo
Feng Shi
Qing-Xia Fan
Liu-Xing Wang
Xiao-Bing Chen
Su-Xia Luo
author_sort Liang-Yu Bie
title Analysis of cyclin E co-expression genes reveals nuclear transcription factor Y subunit alpha is an oncogene in gastric cancer
title_short Analysis of cyclin E co-expression genes reveals nuclear transcription factor Y subunit alpha is an oncogene in gastric cancer
title_full Analysis of cyclin E co-expression genes reveals nuclear transcription factor Y subunit alpha is an oncogene in gastric cancer
title_fullStr Analysis of cyclin E co-expression genes reveals nuclear transcription factor Y subunit alpha is an oncogene in gastric cancer
title_full_unstemmed Analysis of cyclin E co-expression genes reveals nuclear transcription factor Y subunit alpha is an oncogene in gastric cancer
title_sort analysis of cyclin e co-expression genes reveals nuclear transcription factor y subunit alpha is an oncogene in gastric cancer
publisher KeAi Communications Co., Ltd.
publishDate 2019
url https://doaj.org/article/35e896724d9748c68bcfb80d85929713
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