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Identification of key genes and miRNAs markers of papillary thyroid cancer
OBJECTIVE: In this study, crucial genes and microRNAs (miRNAs) associated with the progression, staging, and prognosis of papillary thyroid cancer (PTC) were identified. METHODS: Four PTC datasets, including our own mRNA-sequencing (mRNA-seq) dataset and three public datasets downloaded from Gene Ex...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6230289/ https://www.ncbi.nlm.nih.gov/pubmed/30414611 http://dx.doi.org/10.1186/s40659-018-0188-1 |
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author | Qiu, Jie Zhang, Wenwei Zang, Chuanshan Liu, Xiaomin Liu, Fuxue Ge, Ruifeng Sun, Yan Xia, Qingsheng |
author_facet | Qiu, Jie Zhang, Wenwei Zang, Chuanshan Liu, Xiaomin Liu, Fuxue Ge, Ruifeng Sun, Yan Xia, Qingsheng |
author_sort | Qiu, Jie |
collection | PubMed |
description | OBJECTIVE: In this study, crucial genes and microRNAs (miRNAs) associated with the progression, staging, and prognosis of papillary thyroid cancer (PTC) were identified. METHODS: Four PTC datasets, including our own mRNA-sequencing (mRNA-seq) dataset and three public datasets downloaded from Gene Expression Omnibus and The Cancer Genome Atlas, were used to analyze differentially expressed genes (DEGs) and miRNAs (DEMs) between PTC tumor tissues and paired normal tissues (control). Gene ontology (GO) terms and pathways associated with these DEGs were identified, and protein–protein interactions (PPIs) were analyzed. Additionally, an miRNA-mRNA regulatory network was constructed and the functions of DEMs were explored. Finally, miRNAs/mRNAs associated with tumor staging and prognosis were identified. The expression levels of several key genes and miRNAs were validated by qRT-PCR. RESULTS: Numerous DEGs and DEMs were identified between tumor and control groups in four datasets. The DEGs were significantly enriched in cell adhesion and cancer-related GO terms and pathways. In the constructed PPI network, ITGA2, FN1, ICAM1, TIMP1 and CDH2 were hub proteins. In the miRNA-mRNA negative regulatory networks, miR-204-5p regulated the largest number of target genes, such as TNFRSF12A. miR-146b, miR-204, miR-7-2, and FN1 were associated with tumor stage in PTC, and TNFRSF12A and CLDN1 were related to prognosis. CONCLUSIONS: Our results suggested the important roles of ITGA2, FN1, ICAM1, TIMP1 and CDH2 in the progression of PTC. miR-204-5p, miR-7-2, and miR-146b are potential biomarkers for PTC staging and FN1, CLDN1, and TNFRSF12A may serve as markers of prognosis in PTC. |
format | Online Article Text |
id | pubmed-6230289 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-62302892018-11-19 Identification of key genes and miRNAs markers of papillary thyroid cancer Qiu, Jie Zhang, Wenwei Zang, Chuanshan Liu, Xiaomin Liu, Fuxue Ge, Ruifeng Sun, Yan Xia, Qingsheng Biol Res Research Article OBJECTIVE: In this study, crucial genes and microRNAs (miRNAs) associated with the progression, staging, and prognosis of papillary thyroid cancer (PTC) were identified. METHODS: Four PTC datasets, including our own mRNA-sequencing (mRNA-seq) dataset and three public datasets downloaded from Gene Expression Omnibus and The Cancer Genome Atlas, were used to analyze differentially expressed genes (DEGs) and miRNAs (DEMs) between PTC tumor tissues and paired normal tissues (control). Gene ontology (GO) terms and pathways associated with these DEGs were identified, and protein–protein interactions (PPIs) were analyzed. Additionally, an miRNA-mRNA regulatory network was constructed and the functions of DEMs were explored. Finally, miRNAs/mRNAs associated with tumor staging and prognosis were identified. The expression levels of several key genes and miRNAs were validated by qRT-PCR. RESULTS: Numerous DEGs and DEMs were identified between tumor and control groups in four datasets. The DEGs were significantly enriched in cell adhesion and cancer-related GO terms and pathways. In the constructed PPI network, ITGA2, FN1, ICAM1, TIMP1 and CDH2 were hub proteins. In the miRNA-mRNA negative regulatory networks, miR-204-5p regulated the largest number of target genes, such as TNFRSF12A. miR-146b, miR-204, miR-7-2, and FN1 were associated with tumor stage in PTC, and TNFRSF12A and CLDN1 were related to prognosis. CONCLUSIONS: Our results suggested the important roles of ITGA2, FN1, ICAM1, TIMP1 and CDH2 in the progression of PTC. miR-204-5p, miR-7-2, and miR-146b are potential biomarkers for PTC staging and FN1, CLDN1, and TNFRSF12A may serve as markers of prognosis in PTC. BioMed Central 2018-11-10 /pmc/articles/PMC6230289/ /pubmed/30414611 http://dx.doi.org/10.1186/s40659-018-0188-1 Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Qiu, Jie Zhang, Wenwei Zang, Chuanshan Liu, Xiaomin Liu, Fuxue Ge, Ruifeng Sun, Yan Xia, Qingsheng Identification of key genes and miRNAs markers of papillary thyroid cancer |
title | Identification of key genes and miRNAs markers of papillary thyroid cancer |
title_full | Identification of key genes and miRNAs markers of papillary thyroid cancer |
title_fullStr | Identification of key genes and miRNAs markers of papillary thyroid cancer |
title_full_unstemmed | Identification of key genes and miRNAs markers of papillary thyroid cancer |
title_short | Identification of key genes and miRNAs markers of papillary thyroid cancer |
title_sort | identification of key genes and mirnas markers of papillary thyroid cancer |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6230289/ https://www.ncbi.nlm.nih.gov/pubmed/30414611 http://dx.doi.org/10.1186/s40659-018-0188-1 |
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