Construction of a ceRNA network of hub genes affecting immune infiltration in ovarian cancer identified by WGCNA

BACKGROUND: Ovarian cancer is the leading cause of death among gynecological malignancies. Immunotherapy has demonstrated potential effects in ovarian cancer. However, few studies on immune-related prognostic signatures in ovarian cancer have been reported. This study aimed to identify hub genes ass...

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Autores principales: Su, Rongjia, Jin, Chengjuan, Zhou, Lina, Cao, Yannan, Kuang, Menghua, Li, Linxia, Xiang, Jiangdong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8404317/
https://www.ncbi.nlm.nih.gov/pubmed/34461858
http://dx.doi.org/10.1186/s12885-021-08711-w
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author Su, Rongjia
Jin, Chengjuan
Zhou, Lina
Cao, Yannan
Kuang, Menghua
Li, Linxia
Xiang, Jiangdong
author_facet Su, Rongjia
Jin, Chengjuan
Zhou, Lina
Cao, Yannan
Kuang, Menghua
Li, Linxia
Xiang, Jiangdong
author_sort Su, Rongjia
collection PubMed
description BACKGROUND: Ovarian cancer is the leading cause of death among gynecological malignancies. Immunotherapy has demonstrated potential effects in ovarian cancer. However, few studies on immune-related prognostic signatures in ovarian cancer have been reported. This study aimed to identify hub genes associated with immune infiltrates to provide insight into the immune regulatory mechanisms in ovarian cancer. METHODS: Raw data and clinical information were downloaded from The Cancer Genome Atlas (TCGA) and University of California, Santa Cruz (UCSC) Xena websites. Single-sample gene set enrichment analysis (ssGSEA) and weighted gene co-expression network analysis (WGCNA) were used to identify hub genes. Kaplan-Meier analysis and differential expression analysis were applied to explore the real hub genes. RESULTS: Through ssGSEA and WGCNA, 7 hub genes (LY9, CD5, CXCL9, IL2RG, SLAMF1, SLAMF6, and SLAMF7) were identified. Finally, LY9 and SLAMF1 were recognized as the real hub genes in immune infiltrates of ovarian cancer. LY9 and SLAMF1 are classified as SLAM family receptors involved in the activation of hematopoietic cells and the pathogenesis of multiple malignancies. Furthermore, 12 lncRNAs and 43 miRNAs significantly related to the 2 hub genes were applied to construct a lncRNA-miRNA-mRNA ceRNA network. The lncRNA-miRNA-mRNA ceRNA network shows upstream regulatory sites of the 2 hub genes. CONCLUSIONS: These findings improve our understanding of the regulatory mechanism of and reveal potential immune checkpoints for immunotherapy for ovarian cancer.
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spelling pubmed-84043172021-08-31 Construction of a ceRNA network of hub genes affecting immune infiltration in ovarian cancer identified by WGCNA Su, Rongjia Jin, Chengjuan Zhou, Lina Cao, Yannan Kuang, Menghua Li, Linxia Xiang, Jiangdong BMC Cancer Research Article BACKGROUND: Ovarian cancer is the leading cause of death among gynecological malignancies. Immunotherapy has demonstrated potential effects in ovarian cancer. However, few studies on immune-related prognostic signatures in ovarian cancer have been reported. This study aimed to identify hub genes associated with immune infiltrates to provide insight into the immune regulatory mechanisms in ovarian cancer. METHODS: Raw data and clinical information were downloaded from The Cancer Genome Atlas (TCGA) and University of California, Santa Cruz (UCSC) Xena websites. Single-sample gene set enrichment analysis (ssGSEA) and weighted gene co-expression network analysis (WGCNA) were used to identify hub genes. Kaplan-Meier analysis and differential expression analysis were applied to explore the real hub genes. RESULTS: Through ssGSEA and WGCNA, 7 hub genes (LY9, CD5, CXCL9, IL2RG, SLAMF1, SLAMF6, and SLAMF7) were identified. Finally, LY9 and SLAMF1 were recognized as the real hub genes in immune infiltrates of ovarian cancer. LY9 and SLAMF1 are classified as SLAM family receptors involved in the activation of hematopoietic cells and the pathogenesis of multiple malignancies. Furthermore, 12 lncRNAs and 43 miRNAs significantly related to the 2 hub genes were applied to construct a lncRNA-miRNA-mRNA ceRNA network. The lncRNA-miRNA-mRNA ceRNA network shows upstream regulatory sites of the 2 hub genes. CONCLUSIONS: These findings improve our understanding of the regulatory mechanism of and reveal potential immune checkpoints for immunotherapy for ovarian cancer. BioMed Central 2021-08-30 /pmc/articles/PMC8404317/ /pubmed/34461858 http://dx.doi.org/10.1186/s12885-021-08711-w Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Su, Rongjia
Jin, Chengjuan
Zhou, Lina
Cao, Yannan
Kuang, Menghua
Li, Linxia
Xiang, Jiangdong
Construction of a ceRNA network of hub genes affecting immune infiltration in ovarian cancer identified by WGCNA
title Construction of a ceRNA network of hub genes affecting immune infiltration in ovarian cancer identified by WGCNA
title_full Construction of a ceRNA network of hub genes affecting immune infiltration in ovarian cancer identified by WGCNA
title_fullStr Construction of a ceRNA network of hub genes affecting immune infiltration in ovarian cancer identified by WGCNA
title_full_unstemmed Construction of a ceRNA network of hub genes affecting immune infiltration in ovarian cancer identified by WGCNA
title_short Construction of a ceRNA network of hub genes affecting immune infiltration in ovarian cancer identified by WGCNA
title_sort construction of a cerna network of hub genes affecting immune infiltration in ovarian cancer identified by wgcna
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8404317/
https://www.ncbi.nlm.nih.gov/pubmed/34461858
http://dx.doi.org/10.1186/s12885-021-08711-w
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