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Identification and functional analysis of differentially expressed genes in poorly differentiated hepatocellular carcinoma using RNA-seq

Poorly differentiated (PD) hepatocellular carcinoma (HCC) has a worse prognosis compared to moderately differentiated (MD) and well differentiated (WD) HCC. We aimed to identify differentially expressed genes (DEGs) to explore the mechanism of PD HCC. Transcriptome sequencing was performed on tumor...

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Autores principales: Huang, Yi, Pan, Jianbo, Chen, Dunyan, Zheng, Jiaying, Qiu, Funan, Li, Feng, Wu, Yanan, Wu, Wenbing, Huang, Xiaoli, Qian, Jiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Impact Journals LLC 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5482631/
https://www.ncbi.nlm.nih.gov/pubmed/28415592
http://dx.doi.org/10.18632/oncotarget.16415
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author Huang, Yi
Pan, Jianbo
Chen, Dunyan
Zheng, Jiaying
Qiu, Funan
Li, Feng
Wu, Yanan
Wu, Wenbing
Huang, Xiaoli
Qian, Jiang
author_facet Huang, Yi
Pan, Jianbo
Chen, Dunyan
Zheng, Jiaying
Qiu, Funan
Li, Feng
Wu, Yanan
Wu, Wenbing
Huang, Xiaoli
Qian, Jiang
author_sort Huang, Yi
collection PubMed
description Poorly differentiated (PD) hepatocellular carcinoma (HCC) has a worse prognosis compared to moderately differentiated (MD) and well differentiated (WD) HCC. We aimed to identify differentially expressed genes (DEGs) to explore the mechanism of PD HCC. Transcriptome sequencing was performed on tumor and adjacent non-tumorous tissues of PD, MD and WD HCC patients (3 for each group). DEGs were thus identified and functionally analyzed. Further RT-PCR was performed to validate DEGs specific for PD HCC in 47 pairs of samples (15 for PD, 18 for MD, 14 for WD). A total of 681 PD DEGs were detected, including 368 up-regulated and 313 down-regulated genes. Less DEGs were found for MD and especially for WD HCC. Through bioinformatics analysis, PD HCC DEGs were enriched in liver tissue and liver cancer cells, and in biological process and pathway including metabolism, cell cycle, translation and blood coagulation. Potential drugs and genetic perturbations were found to reverse the cancer condition. The RT-PCR results showed consistency with RNA-seq in the validation of 4 DEGs specific for PD HCC. This study detected and validated DEGs of PD HCC, which provides useful information on molecular mechanism of PD HCC for development of new biomarkers, therapeutic targets and drugs.
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spelling pubmed-54826312017-06-27 Identification and functional analysis of differentially expressed genes in poorly differentiated hepatocellular carcinoma using RNA-seq Huang, Yi Pan, Jianbo Chen, Dunyan Zheng, Jiaying Qiu, Funan Li, Feng Wu, Yanan Wu, Wenbing Huang, Xiaoli Qian, Jiang Oncotarget Research Paper Poorly differentiated (PD) hepatocellular carcinoma (HCC) has a worse prognosis compared to moderately differentiated (MD) and well differentiated (WD) HCC. We aimed to identify differentially expressed genes (DEGs) to explore the mechanism of PD HCC. Transcriptome sequencing was performed on tumor and adjacent non-tumorous tissues of PD, MD and WD HCC patients (3 for each group). DEGs were thus identified and functionally analyzed. Further RT-PCR was performed to validate DEGs specific for PD HCC in 47 pairs of samples (15 for PD, 18 for MD, 14 for WD). A total of 681 PD DEGs were detected, including 368 up-regulated and 313 down-regulated genes. Less DEGs were found for MD and especially for WD HCC. Through bioinformatics analysis, PD HCC DEGs were enriched in liver tissue and liver cancer cells, and in biological process and pathway including metabolism, cell cycle, translation and blood coagulation. Potential drugs and genetic perturbations were found to reverse the cancer condition. The RT-PCR results showed consistency with RNA-seq in the validation of 4 DEGs specific for PD HCC. This study detected and validated DEGs of PD HCC, which provides useful information on molecular mechanism of PD HCC for development of new biomarkers, therapeutic targets and drugs. Impact Journals LLC 2017-03-21 /pmc/articles/PMC5482631/ /pubmed/28415592 http://dx.doi.org/10.18632/oncotarget.16415 Text en Copyright: © 2017 Huang et al. http://creativecommons.org/licenses/by/3.0/ This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) (CC-BY), which permits unrestricted use and redistribution provided that the original author and source are credited.
spellingShingle Research Paper
Huang, Yi
Pan, Jianbo
Chen, Dunyan
Zheng, Jiaying
Qiu, Funan
Li, Feng
Wu, Yanan
Wu, Wenbing
Huang, Xiaoli
Qian, Jiang
Identification and functional analysis of differentially expressed genes in poorly differentiated hepatocellular carcinoma using RNA-seq
title Identification and functional analysis of differentially expressed genes in poorly differentiated hepatocellular carcinoma using RNA-seq
title_full Identification and functional analysis of differentially expressed genes in poorly differentiated hepatocellular carcinoma using RNA-seq
title_fullStr Identification and functional analysis of differentially expressed genes in poorly differentiated hepatocellular carcinoma using RNA-seq
title_full_unstemmed Identification and functional analysis of differentially expressed genes in poorly differentiated hepatocellular carcinoma using RNA-seq
title_short Identification and functional analysis of differentially expressed genes in poorly differentiated hepatocellular carcinoma using RNA-seq
title_sort identification and functional analysis of differentially expressed genes in poorly differentiated hepatocellular carcinoma using rna-seq
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5482631/
https://www.ncbi.nlm.nih.gov/pubmed/28415592
http://dx.doi.org/10.18632/oncotarget.16415
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