Comprehensive analysis of key genes, microRNAs and long non‐coding RNAs in hepatocellular carcinoma
Human hepatocellular carcinoma (HCC) is a common aggressive cancer whose molecular mechanism remains elusive. We aimed to identify the key genes, microRNAs (miRNAs) and long non‐coding RNAs (lncRNAs) involved with HCC. We obtained mRNA, miRNA and lncRNA profiles for HCC from The Cancer Genome Atlas...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2018-09-01
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| Series: | FEBS Open Bio |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/2211-5463.12483 |
| _version_ | 1797870981329453056 |
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| author | Baoqi Shi Xuejun Zhang Lumeng Chao Yu Zheng Yongsheng Tan Liang Wang Wei Zhang |
| author_facet | Baoqi Shi Xuejun Zhang Lumeng Chao Yu Zheng Yongsheng Tan Liang Wang Wei Zhang |
| author_sort | Baoqi Shi |
| collection | DOAJ |
| description | Human hepatocellular carcinoma (HCC) is a common aggressive cancer whose molecular mechanism remains elusive. We aimed to identify the key genes, microRNAs (miRNAs) and long non‐coding RNAs (lncRNAs) involved with HCC. We obtained mRNA, miRNA and lncRNA profiles for HCC from The Cancer Genome Atlas and then identified differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs) and lncRNAs (DElncRNAs). We performed functional annotation of DEmRNAs and then constructed HCC‐specific DEmiRNA–DEmRNA, DEmiRNA–DElncRNA and DElncRNA–DEmiRNA–DEmRNA interaction networks. We searched for nearby target cis‐DEmRNAs of DElncRNAs and performed receiver operating characteristic and survival analyses. A total of 1239 DEmRNAs, 33 DEmiRNAs and 167 DElncRNAs in HCC were obtained. Retinol metabolism [false discovery rate (FDR) = 7.02 × 10−14] and metabolism of xenobiotics by cytochrome P450 (FDR = 7.30 × 10−11) were two significantly enriched pathways in HCC. We obtained 545 DEmiRNA–DEmRNA pairs that consisted of 258 DEmRNAs and 28 DEmiRNAs in HCC. mir‐424, miR‐93 and miR‐3607 are three hub DEmiRNAs of the HCC‐specific DEmiRNA–DEmRNA interaction network. HAND2‐AS1/ENSG00000232855–miR‐93–LRAT/RND3, ENSG00000232855–miR‐877–RCAN1 and ENSG00000232855–miR‐224–RND3 interactions were found in the HCC‐specific DElncRNA–DEmiRNA–DEmRNA interaction network. A total of three DElncRNA–nearby target DEmRNA pairs (HCG25–KIFC1, LOC105378687–CDC20 and LOC101927043–EPCAM) in HCC were obtained. Diagnostic and prognostic values of several selected DElncRNAs, DEmRNAs and DEmiRNAs for HCC were assessed. Our study identified several DEmRNAs, DEmiRNAs and DElncRNAs with great diagnostic or prognostic value for HCC, which may facilitate studies into the molecular mechanisms, and development of potential biomarkers and therapeutic target sites for HCC. |
| first_indexed | 2024-04-10T00:37:01Z |
| format | Article |
| id | doaj.art-04ffbd494dd2428693c26b9f307c6377 |
| institution | Directory Open Access Journal |
| issn | 2211-5463 |
| language | English |
| last_indexed | 2024-04-10T00:37:01Z |
| publishDate | 2018-09-01 |
| publisher | Wiley |
| record_format | Article |
| series | FEBS Open Bio |
| spelling | doaj.art-04ffbd494dd2428693c26b9f307c63772023-03-14T13:05:47ZengWileyFEBS Open Bio2211-54632018-09-01891424143610.1002/2211-5463.12483Comprehensive analysis of key genes, microRNAs and long non‐coding RNAs in hepatocellular carcinomaBaoqi Shi0Xuejun Zhang1Lumeng Chao2Yu Zheng3Yongsheng Tan4Liang Wang5Wei Zhang6Department of Intervention Inner Mongolia People's Hospital Hohhot ChinaDepartment of Intervention Inner Mongolia People's Hospital Hohhot ChinaDepartment of Intervention Inner Mongolia People's Hospital Hohhot ChinaDepartment of Intervention Inner Mongolia People's Hospital Hohhot ChinaDepartment of Intervention Inner Mongolia People's Hospital Hohhot ChinaDepartment of Intervention Inner Mongolia People's Hospital Hohhot ChinaDepartment of Intervention Inner Mongolia People's Hospital Hohhot ChinaHuman hepatocellular carcinoma (HCC) is a common aggressive cancer whose molecular mechanism remains elusive. We aimed to identify the key genes, microRNAs (miRNAs) and long non‐coding RNAs (lncRNAs) involved with HCC. We obtained mRNA, miRNA and lncRNA profiles for HCC from The Cancer Genome Atlas and then identified differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs) and lncRNAs (DElncRNAs). We performed functional annotation of DEmRNAs and then constructed HCC‐specific DEmiRNA–DEmRNA, DEmiRNA–DElncRNA and DElncRNA–DEmiRNA–DEmRNA interaction networks. We searched for nearby target cis‐DEmRNAs of DElncRNAs and performed receiver operating characteristic and survival analyses. A total of 1239 DEmRNAs, 33 DEmiRNAs and 167 DElncRNAs in HCC were obtained. Retinol metabolism [false discovery rate (FDR) = 7.02 × 10−14] and metabolism of xenobiotics by cytochrome P450 (FDR = 7.30 × 10−11) were two significantly enriched pathways in HCC. We obtained 545 DEmiRNA–DEmRNA pairs that consisted of 258 DEmRNAs and 28 DEmiRNAs in HCC. mir‐424, miR‐93 and miR‐3607 are three hub DEmiRNAs of the HCC‐specific DEmiRNA–DEmRNA interaction network. HAND2‐AS1/ENSG00000232855–miR‐93–LRAT/RND3, ENSG00000232855–miR‐877–RCAN1 and ENSG00000232855–miR‐224–RND3 interactions were found in the HCC‐specific DElncRNA–DEmiRNA–DEmRNA interaction network. A total of three DElncRNA–nearby target DEmRNA pairs (HCG25–KIFC1, LOC105378687–CDC20 and LOC101927043–EPCAM) in HCC were obtained. Diagnostic and prognostic values of several selected DElncRNAs, DEmRNAs and DEmiRNAs for HCC were assessed. Our study identified several DEmRNAs, DEmiRNAs and DElncRNAs with great diagnostic or prognostic value for HCC, which may facilitate studies into the molecular mechanisms, and development of potential biomarkers and therapeutic target sites for HCC.https://doi.org/10.1002/2211-5463.12483hepatocellular carcinomalong non‐coding RNAmiRNAmRNATCGA |
| spellingShingle | Baoqi Shi Xuejun Zhang Lumeng Chao Yu Zheng Yongsheng Tan Liang Wang Wei Zhang Comprehensive analysis of key genes, microRNAs and long non‐coding RNAs in hepatocellular carcinoma FEBS Open Bio hepatocellular carcinoma long non‐coding RNA miRNA mRNA TCGA |
| title | Comprehensive analysis of key genes, microRNAs and long non‐coding RNAs in hepatocellular carcinoma |
| title_full | Comprehensive analysis of key genes, microRNAs and long non‐coding RNAs in hepatocellular carcinoma |
| title_fullStr | Comprehensive analysis of key genes, microRNAs and long non‐coding RNAs in hepatocellular carcinoma |
| title_full_unstemmed | Comprehensive analysis of key genes, microRNAs and long non‐coding RNAs in hepatocellular carcinoma |
| title_short | Comprehensive analysis of key genes, microRNAs and long non‐coding RNAs in hepatocellular carcinoma |
| title_sort | comprehensive analysis of key genes micrornas and long non coding rnas in hepatocellular carcinoma |
| topic | hepatocellular carcinoma long non‐coding RNA miRNA mRNA TCGA |
| url | https://doi.org/10.1002/2211-5463.12483 |
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