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Identification of potential novel differentially-expressed genes and their role in invasion and migration in renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) remains one of the most common cancer types globally, and while it has been extensively studied, the molecular basis for its pathology remains incompletely understood. Herein, we profiled three previously published datasets (GSE66272, GSE100666, and GSE105261)...

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Autores principales: Shi, Shen-Nan, Qin, Xia, Wang, Shuo, Wang, Wen-Fu, Zhu, Yao-Feng, Lin, Yu, Zhou, Zun-Lin, Shi, Ben-Kang, Liu, Xi-Gao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Impact Journals 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7288970/
https://www.ncbi.nlm.nih.gov/pubmed/32420905
http://dx.doi.org/10.18632/aging.103192
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author Shi, Shen-Nan
Qin, Xia
Wang, Shuo
Wang, Wen-Fu
Zhu, Yao-Feng
Lin, Yu
Zhou, Zun-Lin
Shi, Ben-Kang
Liu, Xi-Gao
author_facet Shi, Shen-Nan
Qin, Xia
Wang, Shuo
Wang, Wen-Fu
Zhu, Yao-Feng
Lin, Yu
Zhou, Zun-Lin
Shi, Ben-Kang
Liu, Xi-Gao
author_sort Shi, Shen-Nan
collection PubMed
description Clear cell renal cell carcinoma (ccRCC) remains one of the most common cancer types globally, and while it has been extensively studied, the molecular basis for its pathology remains incompletely understood. Herein, we profiled three previously published datasets (GSE66272, GSE100666, and GSE105261) in a single integrated analysis aimed at identifying disease-associated patterns of gene expression that may offer mechanistic insight into the drivers of this disease. We pooled expression data from 39 normal kidney samples and 39 kidney tumors, leading us to identify 310 differentially expressed genes (DEGs) that were linked to kidney cancer in all three analyzed datasets. Of these genes, 133 and 177 were up- and down-regulated, respectively, in cancer samples. We then incorporated these DEGs into a protein-protein interaction network with the STRING and Cytoscape tools, and we were able to identify signaling pathways significantly enriched for these DEGs. The relationship between DEG expression and ccRCC patient survival was further evaluated using a Kaplan-Meier approach, leading us to identify TIMP1 as an independent prognostic factor in ccRCC patients. When TIMP1 expression was disrupted in ccRCC cell lines, this impaired their migratory and invasive capabilities. In summary, we employed an integrative bioinformatics approach to identify ccRCC-related DEGs and associated signaling pathways. Together these findings offer novel insight into the mechanistic basis for ccRCC, potentially helping to identify novel therapeutic targets for the treatment of this deadly disease.
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spelling pubmed-72889702020-06-22 Identification of potential novel differentially-expressed genes and their role in invasion and migration in renal cell carcinoma Shi, Shen-Nan Qin, Xia Wang, Shuo Wang, Wen-Fu Zhu, Yao-Feng Lin, Yu Zhou, Zun-Lin Shi, Ben-Kang Liu, Xi-Gao Aging (Albany NY) Research Paper Clear cell renal cell carcinoma (ccRCC) remains one of the most common cancer types globally, and while it has been extensively studied, the molecular basis for its pathology remains incompletely understood. Herein, we profiled three previously published datasets (GSE66272, GSE100666, and GSE105261) in a single integrated analysis aimed at identifying disease-associated patterns of gene expression that may offer mechanistic insight into the drivers of this disease. We pooled expression data from 39 normal kidney samples and 39 kidney tumors, leading us to identify 310 differentially expressed genes (DEGs) that were linked to kidney cancer in all three analyzed datasets. Of these genes, 133 and 177 were up- and down-regulated, respectively, in cancer samples. We then incorporated these DEGs into a protein-protein interaction network with the STRING and Cytoscape tools, and we were able to identify signaling pathways significantly enriched for these DEGs. The relationship between DEG expression and ccRCC patient survival was further evaluated using a Kaplan-Meier approach, leading us to identify TIMP1 as an independent prognostic factor in ccRCC patients. When TIMP1 expression was disrupted in ccRCC cell lines, this impaired their migratory and invasive capabilities. In summary, we employed an integrative bioinformatics approach to identify ccRCC-related DEGs and associated signaling pathways. Together these findings offer novel insight into the mechanistic basis for ccRCC, potentially helping to identify novel therapeutic targets for the treatment of this deadly disease. Impact Journals 2020-05-18 /pmc/articles/PMC7288970/ /pubmed/32420905 http://dx.doi.org/10.18632/aging.103192 Text en Copyright © 2020 Shi et al. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Paper
Shi, Shen-Nan
Qin, Xia
Wang, Shuo
Wang, Wen-Fu
Zhu, Yao-Feng
Lin, Yu
Zhou, Zun-Lin
Shi, Ben-Kang
Liu, Xi-Gao
Identification of potential novel differentially-expressed genes and their role in invasion and migration in renal cell carcinoma
title Identification of potential novel differentially-expressed genes and their role in invasion and migration in renal cell carcinoma
title_full Identification of potential novel differentially-expressed genes and their role in invasion and migration in renal cell carcinoma
title_fullStr Identification of potential novel differentially-expressed genes and their role in invasion and migration in renal cell carcinoma
title_full_unstemmed Identification of potential novel differentially-expressed genes and their role in invasion and migration in renal cell carcinoma
title_short Identification of potential novel differentially-expressed genes and their role in invasion and migration in renal cell carcinoma
title_sort identification of potential novel differentially-expressed genes and their role in invasion and migration in renal cell carcinoma
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7288970/
https://www.ncbi.nlm.nih.gov/pubmed/32420905
http://dx.doi.org/10.18632/aging.103192
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